Ticket #4877: full_log.txt

File full_log.txt, 422.2 KB (added by Tom Goddard, 4 years ago)
Line 
1{{{
2The following bug report has been submitted:
3Platform: Linux-5.10.0-1034-oem-x86_64-with-glibc2.14
4ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
5Description
6(Describe the actions that caused this problem to occur here)
7
8Log:
9UCSF ChimeraX version: 1.2.5 (2021-05-24)
10© 2016-2021 Regents of the University of California. All rights reserved.
11How to cite UCSF ChimeraX
12
13> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/ucsf-commands.cxc
14
15> set bgColor white
16
17> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3EI4.pdbqt
18
19Chain information for 3EI4.pdbqt #1
20---
21Chain | Description
22A C E | No description available
23B D F | No description available
24
25Opened 3EI4.pdbqt containing 1 structures (70284 atoms, 71031 bonds)
26
27> wait 5
28
29> hide surfaces
30
31> hide atoms
32
33> show cartoons
34
35> wait 5
36
37> addh
38
39Summary of feedback from adding hydrogens to 3EI4.pdbqt #1
40---
41warnings | Not adding hydrogens to /A GLU 368 CB because it is missing heavy-
42atom bond partners
43Not adding hydrogens to /A ARG 369 CB because it is missing heavy-atom bond
44partners
45Not adding hydrogens to /A GLN 759 CB because it is missing heavy-atom bond
46partners
47Not adding hydrogens to /A GLU 779 CB because it is missing heavy-atom bond
48partners
49Not adding hydrogens to /A THR 780 CB because it is missing heavy-atom bond
50partners
5149 messages similar to the above omitted
52notes | No usable SEQRES records for 3EI4.pdbqt (#1) chain A; guessing termini
53instead
54No usable SEQRES records for 3EI4.pdbqt (#1) chain B; guessing termini instead
55No usable SEQRES records for 3EI4.pdbqt (#1) chain C; guessing termini instead
56No usable SEQRES records for 3EI4.pdbqt (#1) chain D; guessing termini instead
57No usable SEQRES records for 3EI4.pdbqt (#1) chain E; guessing termini instead
581 messages similar to the above omitted
59Chain-initial residues that are actual N termini: /A MET 1, /B TRP 54, /C MET
601, /D TRP 54, /E MET 1, /F TRP 54
61Chain-initial residues that are not actual N termini:
62Chain-final residues that are actual C termini: /A HIS 1140, /B GLU 421, /C
63HIS 1140, /D GLU 421, /E HIS 1140, /F GLU 421
64Chain-final residues that are not actual C termini:
652812 hydrogen bonds
66114 hydrogens added
67
68
69> wait 5
70
71> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3EI4--
72> WRM-16.result.pdbqt
73
74Summary of feedback from opening
75/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3EI4--WRM-16.result.pdbqt
76---
77warnings | Ignored bad PDB record found on line 2
78REMARK VINA RESULT: -8.8 0.000 0.000
79
80Ignored bad PDB record found on line 3
81REMARK 5 active torsions:
82
83Ignored bad PDB record found on line 4
84REMARK status: ('A' for Active; 'I' for Inactive)
85
86Ignored bad PDB record found on line 5
87REMARK 1 A between atoms: C_9 and O_15
88
89Ignored bad PDB record found on line 6
90REMARK 2 A between atoms: C_10 and O_17
91
92184 messages similar to the above omitted
93
94Opened 3EI4--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
95bonds)
96
97> wait 5
98
99> close #2.2-9
100
101> wait 5
102
103> contacts :UNL radius 0.05 log true saveFile
104> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
105> WRM-16.contacts.txt
106
107
108 Allowed overlap: -0.4
109 H-bond overlap reduction: 0.4
110 Ignore contacts between atoms separated by 4 bonds or less
111 Detect intra-residue contacts: False
112 Detect intra-molecule contacts: True
113
114 40 contacts
115 atom1 atom2 overlap distance
116 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C ARG 639 HE 0.326 2.554
117 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 458 O 0.049 3.311
118 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C ARG 639 NE -0.005 3.510
119 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C LEU 410 HN -0.006 2.886
120 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 HB2 -0.009 2.889
121 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 638 O -0.028 3.388
122 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 HN -0.045 2.065
123 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 O -0.050 3.410
124 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C LEU 410 O -0.056 3.416
125 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ARG 639 HG2 -0.071 2.831
126 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C VAL 637 CG1 -0.071 3.531
127 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C VAL 637 2HG1 -0.089 2.509
128 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 C -0.092 3.672
129 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 592 HB2 -0.115 2.995
130 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 592 CB -0.121 3.701
131 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 HD2 -0.131 2.891
132 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C SER 590 HA -0.193 2.613
133 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 HB2 -0.227 3.107
134 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C TYR 678 HD2 -0.237 2.997
135 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ARG 639 CG -0.240 3.700
136 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C TYR 678 CD2 -0.246 3.706
137 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ILE 591 O -0.258 3.618
138 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ARG 639 HE -0.271 3.031
139 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 O -0.284 3.184
140 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 O -0.286 3.226
141 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 CD2 -0.291 3.751
142 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 CD2 -0.291 3.751
143 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 638 HB2 -0.296 3.176
144 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 HD2 -0.312 3.072
145 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C MET 679 O -0.331 3.691
146 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C ARG 639 2HH2 -0.331 3.211
147 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C SER 590 CA -0.344 3.464
148 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C VAL 637 2HG1 -0.350 3.110
149 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 638 C -0.357 3.937
150 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 CB -0.367 3.947
151 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 N -0.374 3.019
152 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C VAL 637 CG1 -0.386 3.696
153 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C LEU 410 N -0.387 3.892
154 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 CB -0.394 3.974
155 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 592 HB1 -0.394 3.274
156
157
158
15940 contacts
160
161> hbonds :UNL showDist true radius 0.05 log true saveFile
162> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
163> WRM-16.hbonds.txt
164
165
166 Finding intermodel H-bonds
167 Finding intramodel H-bonds
168 Constraints relaxed by 0.4 angstroms and 20 degrees
169 Models used:
170 1 3EI4.pdbqt
171 2.1 3EI4--WRM-16.result.pdbqt
172
173 1 H-bonds
174 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
175 3EI4.pdbqt #1/C ILE 591 N 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 HN 3.019 2.065
176
177
178
1791 hydrogen bonds found
180
181> select :UNL
182
18328 atoms, 31 bonds, 1 residue, 1 model selected
184
185> label sel text "Ligand "
186
187> label height 1
188
189> ~select
190
191Nothing selected
192
193> 2dlabels text "Binding Energy: -8.8 kcal/mol" color red size 18 xpos .03
194> ypos .95
195
196> 2dlabels text "3EI4 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
197
198> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
199> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
200> true
201
202> select :UNL
203
20428 atoms, 31 bonds, 1 residue, 1 model selected
205
206> view sel
207
208> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
209> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
210> true
211
212> close
213
214> wait 5
215
216> set bgColor white
217
218> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2PA2.pdbqt
219
220Chain information for 2PA2.pdbqt #1
221---
222Chain | Description
223A B | No description available
224
225Opened 2PA2.pdbqt containing 1 structures (3578 atoms, 3614 bonds)
226
227> wait 5
228
229> hide surfaces
230
231> hide atoms
232
233> show cartoons
234
235> wait 5
236
237> addh
238
239Summary of feedback from adding hydrogens to 2PA2.pdbqt #1
240---
241notes | No usable SEQRES records for 2PA2.pdbqt (#1) chain A; guessing termini
242instead
243No usable SEQRES records for 2PA2.pdbqt (#1) chain B; guessing termini instead
244Chain-initial residues that are actual N termini: /A LYS 40, /B LYS 40
245Chain-initial residues that are not actual N termini: /A GLY 124, /B GLY 124
246Chain-final residues that are actual C termini: /A PHE 176, /B PHE 176
247Chain-final residues that are not actual C termini: /A PHE 94, /B PHE 94
248173 hydrogen bonds
249Adding 'H' to /A GLY 124
250Adding 'H' to /B GLY 124
251/A PHE 94 is not terminus, removing H atom from 'C'
252/B PHE 94 is not terminus, removing H atom from 'C'
2530 hydrogens added
254
255
256> wait 5
257
258> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2PA2--
259> WRM-16.result.pdbqt
260
261Summary of feedback from opening
262/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2PA2--WRM-16.result.pdbqt
263---
264warnings | Ignored bad PDB record found on line 2
265REMARK VINA RESULT: -8.4 0.000 0.000
266
267Ignored bad PDB record found on line 3
268REMARK 5 active torsions:
269
270Ignored bad PDB record found on line 4
271REMARK status: ('A' for Active; 'I' for Inactive)
272
273Ignored bad PDB record found on line 5
274REMARK 1 A between atoms: C_9 and O_15
275
276Ignored bad PDB record found on line 6
277REMARK 2 A between atoms: C_10 and O_17
278
279184 messages similar to the above omitted
280
281Opened 2PA2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
282bonds)
283
284> wait 5
285
286> close #2.2-9
287
288> wait 5
289
290> contacts :UNL radius 0.05 log true saveFile
291> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
292> WRM-16.contacts.txt
293
294
295 Allowed overlap: -0.4
296 H-bond overlap reduction: 0.4
297 Ignore contacts between atoms separated by 4 bonds or less
298 Detect intra-residue contacts: False
299 Detect intra-molecule contacts: True
300
301 42 contacts
302 atom1 atom2 overlap distance
303 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 1HH1 0.226 2.384
304 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH1 0.203 1.817
305 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 0.129 2.481
306 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B ARG 128 HB2 0.110 2.650
307 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE1 0.107 2.773
308 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HB2 0.007 2.753
309 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 0.001 2.759
310 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HB2 -0.038 2.648
311 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 -0.039 2.649
312 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 1HH2 -0.042 2.922
313 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH2 -0.049 2.109
314 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2PA2.pdbqt #1/B HIS 92 O -0.078 3.438
315 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 CE1 -0.094 3.674
316 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 1HH2 -0.105 2.985
317 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A VAL 43 CG1 -0.107 3.687
318 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A PRO 47 HA -0.111 2.531
319 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HD1 -0.114 2.874
320 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HD1 -0.119 2.879
321 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2PA2.pdbqt #1/B ARG 128 O -0.121 3.481
322 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/B HIS 130 HE1 -0.121 2.581
323 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 NH1 -0.139 2.784
324 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 NH1 -0.150 3.385
325 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 NE2 -0.172 3.557
326 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HB2 -0.175 2.785
327 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CD1 -0.211 3.671
328 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A LYS 169 O -0.229 3.319
329 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 NH2 -0.235 3.740
330 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A VAL 43 O -0.237 3.137
331 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 NE2 -0.243 3.478
332 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B ARG 128 HD2 -0.251 3.011
333 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CB -0.266 3.576
334 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A TRP 171 HB2 -0.278 2.698
335 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A PRO 47 CB -0.283 3.863
336 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B ARG 128 CB -0.291 3.751
337 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A VAL 43 1HG1 -0.297 3.177
338 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2PA2.pdbqt #1/B HIS 92 HN -0.300 3.180
339 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CD1 -0.306 3.766
340 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CB -0.325 3.785
341 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 NE2 -0.331 3.566
342 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HN -0.354 3.234
343 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A VAL 43 HB -0.364 2.974
344 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 -0.383 3.143
345
346
347
34842 contacts
349
350> hbonds :UNL showDist true radius 0.05 log true saveFile
351> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
352> WRM-16.hbonds.txt
353
354
355 Finding intermodel H-bonds
356 Finding intramodel H-bonds
357 Constraints relaxed by 0.4 angstroms and 20 degrees
358 Models used:
359 1 2PA2.pdbqt
360 2.1 2PA2--WRM-16.result.pdbqt
361
362 4 H-bonds
363 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
364 2PA2.pdbqt #1/A ARG 139 NH1 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH1 3.380 2.525
365 2PA2.pdbqt #1/A ARG 139 NH1 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH1 2.784 1.817
366 2PA2.pdbqt #1/A ARG 139 NH2 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH2 3.087 2.109
367 2PA2.pdbqt #1/A TRP 171 N 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A TRP 171 HN 3.576 2.621
368
369
370
3714 hydrogen bonds found
372
373> select :UNL
374
37528 atoms, 31 bonds, 1 residue, 1 model selected
376
377> label sel text "Ligand "
378
379> label height 1
380
381> ~select
382
383Nothing selected
384
385> 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03
386> ypos .95
387
388> 2dlabels text "2PA2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
389
390> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
391> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
392> true
393
394> select :UNL
395
39628 atoms, 31 bonds, 1 residue, 1 model selected
397
398> view sel
399
400> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
401> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
402> true
403
404> close
405
406> wait 5
407
408> set bgColor white
409
410> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KV2.pdbqt
411
412Chain information for 2KV2.pdbqt #1
413---
414Chain | Description
415A | No description available
416
417Opened 2KV2.pdbqt containing 1 structures (1351 atoms, 1361 bonds)
418
419> wait 5
420
421> hide surfaces
422
423> hide atoms
424
425> show cartoons
426
427> wait 5
428
429> addh
430
431Summary of feedback from adding hydrogens to 2KV2.pdbqt #1
432---
433notes | No usable SEQRES records for 2KV2.pdbqt (#1) chain A; guessing termini
434instead
435Chain-initial residues that are actual N termini: /A GLN 1
436Chain-initial residues that are not actual N termini:
437Chain-final residues that are actual C termini: /A ASP 85
438Chain-final residues that are not actual C termini:
43961 hydrogen bonds
4401 hydrogens added
441
442
443> wait 5
444
445> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KV2--
446> WRM-16.result.pdbqt
447
448Summary of feedback from opening
449/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KV2--WRM-16.result.pdbqt
450---
451warnings | Ignored bad PDB record found on line 2
452REMARK VINA RESULT: -6.4 0.000 0.000
453
454Ignored bad PDB record found on line 3
455REMARK 5 active torsions:
456
457Ignored bad PDB record found on line 4
458REMARK status: ('A' for Active; 'I' for Inactive)
459
460Ignored bad PDB record found on line 5
461REMARK 1 A between atoms: C_9 and O_15
462
463Ignored bad PDB record found on line 6
464REMARK 2 A between atoms: C_10 and O_17
465
466184 messages similar to the above omitted
467
468Opened 2KV2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
469bonds)
470
471> wait 5
472
473> close #2.2-9
474
475> wait 5
476
477> contacts :UNL radius 0.05 log true saveFile
478> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
479> WRM-16.contacts.txt
480
481
482 Allowed overlap: -0.4
483 H-bond overlap reduction: 0.4
484 Ignore contacts between atoms separated by 4 bonds or less
485 Detect intra-residue contacts: False
486 Detect intra-molecule contacts: True
487
488 52 contacts
489 atom1 atom2 overlap distance
490 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HB2 0.640 2.240
491 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HB3 0.469 2.291
492 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CB 0.306 3.274
493 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HD2 0.278 2.482
494 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A THR 80 HB 0.207 2.673
495 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 CE 0.105 3.055
496 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HD2 0.105 2.655
497 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 CB 0.100 3.360
498 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HB2 0.075 2.685
499 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A THR 80 CB 0.039 3.541
500 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CD2 -0.031 3.491
501 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HE3 -0.057 2.817
502 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HD1 -0.060 2.820
503 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CE3 -0.080 3.540
504 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CD1 -0.084 3.544
505 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HZ3 -0.099 2.979
506 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CD1 -0.106 3.686
507 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A THR 80 HB -0.115 2.875
508 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HB2 -0.131 3.011
509 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 HE2 -0.136 2.596
510 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HA -0.165 2.775
511 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HA -0.207 2.817
512 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 CD -0.208 3.668
513 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A THR 80 OG1 -0.214 3.594
514 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CB -0.214 3.674
515 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HB3 -0.227 2.837
516 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CE3 -0.237 3.547
517 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HD2 -0.262 3.142
518 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 C -0.263 3.723
519 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 CE3 -0.272 3.852
520 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 CZ3 -0.273 3.853
521 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 HZ3 -0.277 3.157
522 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 HE3 -0.280 3.160
523 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CB -0.297 3.607
524 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CD2 -0.310 3.890
525 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CB -0.317 3.897
526 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 O -0.323 3.563
527 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 HE2 -0.324 2.744
528 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 75 HB3 -0.325 2.785
529 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 O -0.329 3.569
530 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 75 CB -0.330 3.490
531 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HB2 -0.331 2.941
532 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 O -0.336 3.576
533 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A TRP 79 CG -0.355 3.515
534 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HE3 -0.360 2.970
535 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 NZ -0.373 3.878
536 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CG -0.376 3.956
537 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A VAL 72 3HG2 -0.383 2.803
538 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 HE3 -0.388 2.848
539 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HD2 -0.388 3.148
540 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HB3 -0.391 3.151
541 2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 8 HE2 -0.399 3.009
542
543
544
54552 contacts
546
547> hbonds :UNL showDist true radius 0.05 log true saveFile
548> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
549> WRM-16.hbonds.txt
550
551
552 Finding intermodel H-bonds
553 Finding intramodel H-bonds
554 Constraints relaxed by 0.4 angstroms and 20 degrees
555 Models used:
556 1 2KV2.pdbqt
557 2.1 2KV2--WRM-16.result.pdbqt
558
559 0 H-bonds
560 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
561
562
563
5640 hydrogen bonds found
565
566> select :UNL
567
56828 atoms, 31 bonds, 1 residue, 1 model selected
569
570> label sel text "Ligand "
571
572> label height 1
573
574> ~select
575
576Nothing selected
577
578> 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03
579> ypos .95
580
581> 2dlabels text "2KV2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
582
583> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
584> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
585> true
586
587> select :UNL
588
58928 atoms, 31 bonds, 1 residue, 1 model selected
590
591> view sel
592
593> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
594> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
595> true
596
597> close
598
599> wait 5
600
601> set bgColor white
602
603> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3CO6.pdbqt
604
605Chain information for 3CO6.pdbqt #1
606---
607Chain | Description
608A | No description available
609B | No description available
610C | No description available
611
612Opened 3CO6.pdbqt containing 1 structures (2476 atoms, 2572 bonds)
613
614> wait 5
615
616> hide surfaces
617
618> hide atoms
619
620> show cartoons
621
622> wait 5
623
624> addh
625
626Summary of feedback from adding hydrogens to 3CO6.pdbqt #1
627---
628warnings | Not adding hydrogens to /C LYS 192 CB because it is missing heavy-
629atom bond partners
630Not adding hydrogens to /C LYS 198 CB because it is missing heavy-atom bond
631partners
632Not adding hydrogens to /C ASN 204 CB because it is missing heavy-atom bond
633partners
634Not adding hydrogens to /C GLU 242 CB because it is missing heavy-atom bond
635partners
636notes | No usable SEQRES records for 3CO6.pdbqt (#1) chain A; guessing termini
637instead
638No usable SEQRES records for 3CO6.pdbqt (#1) chain B; guessing termini instead
639No usable SEQRES records for 3CO6.pdbqt (#1) chain C; guessing termini instead
640Chain-initial residues that are actual N termini: /A DT -4, /B DC 13, /C SER
641154
642Chain-initial residues that are not actual N termini:
643Chain-final residues that are actual C termini: /A DG 12, /B DA 28, /C GLY 244
644Chain-final residues that are not actual C termini:
645127 hydrogen bonds
6464 hydrogens added
647
648
649> wait 5
650
651> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3CO6--
652> WRM-16.result.pdbqt
653
654Summary of feedback from opening
655/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3CO6--WRM-16.result.pdbqt
656---
657warnings | Ignored bad PDB record found on line 2
658REMARK VINA RESULT: -9.1 0.000 0.000
659
660Ignored bad PDB record found on line 3
661REMARK 5 active torsions:
662
663Ignored bad PDB record found on line 4
664REMARK status: ('A' for Active; 'I' for Inactive)
665
666Ignored bad PDB record found on line 5
667REMARK 1 A between atoms: C_9 and O_15
668
669Ignored bad PDB record found on line 6
670REMARK 2 A between atoms: C_10 and O_17
671
672184 messages similar to the above omitted
673
674Opened 3CO6--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
675bonds)
676
677> wait 5
678
679> close #2.2-9
680
681> wait 5
682
683> contacts :UNL radius 0.05 log true saveFile
684> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
685> WRM-16.contacts.txt
686
687
688 Allowed overlap: -0.4
689 H-bond overlap reduction: 0.4
690 Ignore contacts between atoms separated by 4 bonds or less
691 Detect intra-residue contacts: False
692 Detect intra-molecule contacts: True
693
694 57 contacts
695 atom1 atom2 overlap distance
696 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3CO6.pdbqt #1/A DT 4 H4' 0.285 2.595
697 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 234 HA 0.279 2.481
698 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C GLN 227 OE1 0.215 3.025
699 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 O3' 0.090 3.290
700 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 2HH1 0.039 2.721
701 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 NH1 0.011 3.374
702 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 C5' 0.002 3.578
703 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 24 H3 0.000 2.880
704 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 O4' -0.016 3.396
705 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 H4' -0.026 2.906
706 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 1H5' -0.041 2.921
707 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 C2 -0.066 3.226
708 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 234 CA -0.080 3.540
709 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H22 -0.090 2.850
710 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H3 -0.095 2.155
711 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C LYS 233 O -0.116 3.356
712 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3CO6.pdbqt #1/A DT 4 C4' -0.123 3.703
713 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H3 -0.125 2.885
714 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 OG -0.180 3.440
715 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H22 -0.187 2.947
716 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 H4' -0.190 2.800
717 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 23 H2 -0.212 2.632
718 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 2H5' -0.212 3.092
719 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 OG -0.222 3.482
720 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 N3 -0.223 2.908
721 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 23 C2 -0.223 3.343
722 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 C4' -0.229 3.809
723 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 C4' -0.230 3.810
724 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H2 -0.237 2.697
725 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 P -0.239 3.990
726 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/A DT 2 O4' -0.260 3.180
727 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/A DT 2 H4' -0.264 2.724
728 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 H4' -0.269 2.879
729 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C LYS 233 O -0.273 3.513
730 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 24 N3 -0.286 3.791
731 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 O4' -0.296 3.216
732 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H2 -0.297 2.717
733 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 C4' -0.299 3.759
734 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C GLN 227 CD -0.302 3.762
735 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 H4' -0.308 2.918
736 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 N3 -0.316 3.701
737 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H4' -0.322 3.202
738 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 N2 -0.323 3.708
739 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 H4' -0.326 3.086
740 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 NH1 -0.332 3.717
741 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 C4 -0.337 3.457
742 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/A DT 2 O2 -0.341 3.281
743 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 2HH1 -0.352 3.112
744 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 O4' -0.360 3.620
745 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 N3 -0.360 3.005
746 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 C5' -0.366 3.946
747 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 C4' -0.374 3.684
748 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 N -0.392 3.777
749 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 C1' -0.394 3.514
750 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 N -0.394 3.779
751 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 OP1 -0.397 3.777
752 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 C4' -0.400 3.980
753
754
755
75657 contacts
757
758> hbonds :UNL showDist true radius 0.05 log true saveFile
759> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
760> WRM-16.hbonds.txt
761
762
763 Finding intermodel H-bonds
764 Finding intramodel H-bonds
765 Constraints relaxed by 0.4 angstroms and 20 degrees
766 Models used:
767 1 3CO6.pdbqt
768 2.1 3CO6--WRM-16.result.pdbqt
769
770 1 H-bonds
771 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
772 3CO6.pdbqt #1/B DA 24 N3 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H3 2.908 2.155
773
774
775
7761 hydrogen bonds found
777
778> select :UNL
779
78028 atoms, 31 bonds, 1 residue, 1 model selected
781
782> label sel text "Ligand "
783
784> label height 1
785
786> ~select
787
788Nothing selected
789
790> 2dlabels text "Binding Energy: -9.1 kcal/mol" color red size 18 xpos .03
791> ypos .95
792
793> 2dlabels text "3CO6 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
794
795> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
796> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
797> true
798
799> select :UNL
800
80128 atoms, 31 bonds, 1 residue, 1 model selected
802
803> view sel
804
805> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
806> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
807> true
808
809> close
810
811> wait 5
812
813> set bgColor white
814
815> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1D7G.pdbqt
816
817Chain information for 1D7G.pdbqt #1
818---
819Chain | Description
820A | No description available
821B | No description available
822C | No description available
823D | No description available
824
825Opened 1D7G.pdbqt containing 1 structures (2929 atoms, 3008 bonds)
826
827> wait 5
828
829> hide surfaces
830
831> hide atoms
832
833> show cartoons
834
835> wait 5
836
837> addh
838
839Summary of feedback from adding hydrogens to 1D7G.pdbqt #1
840---
841warnings | Not adding hydrogens to /A G 5 C2' because it is missing heavy-atom
842bond partners
843Not adding hydrogens to /A C 6 C2' because it is missing heavy-atom bond
844partners
845Not adding hydrogens to /A C 7 C2' because it is missing heavy-atom bond
846partners
847Not adding hydrogens to /A C 8 C2' because it is missing heavy-atom bond
848partners
849Not adding hydrogens to /A A 10 C2' because it is missing heavy-atom bond
850partners
85119 messages similar to the above omitted
852notes | No usable SEQRES records for 1D7G.pdbqt (#1) chain A; guessing termini
853instead
854No usable SEQRES records for 1D7G.pdbqt (#1) chain B; guessing termini instead
855No usable SEQRES records for 1D7G.pdbqt (#1) chain C; guessing termini instead
856No usable SEQRES records for 1D7G.pdbqt (#1) chain D; guessing termini instead
857Chain-initial residues that are actual N termini: /A G 5, /B G 5, /C GLU 1, /D
858SER 1
859Chain-initial residues that are not actual N termini:
860Chain-final residues that are actual C termini: /A C 18, /B C 18, /C THR 59,
861/D LEU 59
862Chain-final residues that are not actual C termini:
863153 hydrogen bonds
8644 hydrogens added
865
866
867> wait 5
868
869> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1D7G--
870> WRM-16.result.pdbqt
871
872Summary of feedback from opening
873/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1D7G--WRM-16.result.pdbqt
874---
875warnings | Ignored bad PDB record found on line 2
876REMARK VINA RESULT: -7.9 0.000 0.000
877
878Ignored bad PDB record found on line 3
879REMARK 5 active torsions:
880
881Ignored bad PDB record found on line 4
882REMARK status: ('A' for Active; 'I' for Inactive)
883
884Ignored bad PDB record found on line 5
885REMARK 1 A between atoms: C_9 and O_15
886
887Ignored bad PDB record found on line 6
888REMARK 2 A between atoms: C_10 and O_17
889
890184 messages similar to the above omitted
891
892Opened 1D7G--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
893bonds)
894
895> wait 5
896
897> close #2.2-9
898
899> wait 5
900
901> contacts :UNL radius 0.05 log true saveFile
902> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
903> WRM-16.contacts.txt
904
905
906 Allowed overlap: -0.4
907 H-bond overlap reduction: 0.4
908 Ignore contacts between atoms separated by 4 bonds or less
909 Detect intra-residue contacts: False
910 Detect intra-molecule contacts: True
911
912 39 contacts
913 atom1 atom2 overlap distance
914 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HE 0.329 2.431
915 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 15 1H2' 0.256 2.624
916 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 HG1 0.119 2.641
917 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 2HH1 0.015 2.005
918 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 NE -0.009 3.394
919 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1D7G.pdbqt #1/D LYS 5 CG -0.009 3.589
920 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HB2 -0.018 2.778
921 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 H7 -0.024 2.044
922 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 H7 -0.025 2.045
923 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1D7G.pdbqt #1/D LYS 5 HG1 -0.045 2.925
924 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 H7 -0.079 2.959
925 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 CZ -0.085 3.245
926 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 15 C2' -0.096 3.676
927 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1D7G.pdbqt #1/D SER 1 O -0.112 3.472
928 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 2HH1 -0.121 2.731
929 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HB2 -0.137 2.897
930 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 N7 -0.144 3.649
931 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B C 18 H41 -0.162 3.042
932 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 NH1 -0.162 3.397
933 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 17 H7 -0.174 2.784
934 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 15 C8 -0.195 3.315
935 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 HG1 -0.207 2.817
936 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 NH1 -0.209 2.894
937 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 H7 -0.210 2.820
938 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 C8 -0.227 3.387
939 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 C8 -0.227 3.807
940 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 CG -0.232 3.692
941 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 N7 -0.234 3.469
942 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 O2P -0.237 3.197
943 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 CB -0.252 3.712
944 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 N -0.277 3.662
945 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 O2P -0.310 3.570
946 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 H8 -0.331 3.211
947 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 NH1 -0.333 2.978
948 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 15 C8 -0.337 3.647
949 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HE -0.343 2.953
950 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 N7 -0.347 2.992
951 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 N7 -0.366 3.011
952 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 O6 -0.397 3.297
953
954
955
95639 contacts
957
958> hbonds :UNL showDist true radius 0.05 log true saveFile
959> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
960> WRM-16.hbonds.txt
961
962
963 Finding intermodel H-bonds
964 Finding intramodel H-bonds
965 Constraints relaxed by 0.4 angstroms and 20 degrees
966 Models used:
967 1 1D7G.pdbqt
968 2.1 1D7G--WRM-16.result.pdbqt
969
970 3 H-bonds
971 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
972 1D7G.pdbqt #1/B G 16 N7 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 H7 2.992 2.045
973 1D7G.pdbqt #1/B G 17 N7 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 H7 3.011 2.044
974 1D7G.pdbqt #1/D ARG 4 NH1 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 2HH1 2.978 2.005
975
976
977
9783 hydrogen bonds found
979
980> select :UNL
981
98228 atoms, 31 bonds, 1 residue, 1 model selected
983
984> label sel text "Ligand "
985
986> label height 1
987
988> ~select
989
990Nothing selected
991
992> 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
993> ypos .95
994
995> 2dlabels text "1D7G WRM-16 Complex" color gray size 18 xpos .03 ypos .91
996
997> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
998> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
999> true
1000
1001> select :UNL
1002
100328 atoms, 31 bonds, 1 residue, 1 model selected
1004
1005> view sel
1006
1007> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
1008> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
1009> true
1010
1011> close
1012
1013> wait 5
1014
1015> set bgColor white
1016
1017> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1GXC.pdbqt
1018
1019Chain information for 1GXC.pdbqt #1
1020---
1021Chain | Description
1022A D G J | No description available
1023B E H K | No description available
1024
1025Opened 1GXC.pdbqt containing 1 structures (8116 atoms, 8224 bonds)
1026
1027> wait 5
1028
1029> hide surfaces
1030
1031> hide atoms
1032
1033> show cartoons
1034
1035> wait 5
1036
1037> addh
1038
1039Summary of feedback from adding hydrogens to 1GXC.pdbqt #1
1040---
1041warnings | Not adding hydrogens to /A ASP 111 CB because it is missing heavy-
1042atom bond partners
1043Not adding hydrogens to /D ASP 111 CB because it is missing heavy-atom bond
1044partners
1045Not adding hydrogens to /G ASP 111 CB because it is missing heavy-atom bond
1046partners
1047Not adding hydrogens to /H ARG 7 CB because it is missing heavy-atom bond
1048partners
1049Not adding hydrogens to /J ASP 111 CB because it is missing heavy-atom bond
1050partners
10511 messages similar to the above omitted
1052notes | No usable SEQRES records for 1GXC.pdbqt (#1) chain A; guessing termini
1053instead
1054No usable SEQRES records for 1GXC.pdbqt (#1) chain B; guessing termini instead
1055No usable SEQRES records for 1GXC.pdbqt (#1) chain D; guessing termini instead
1056No usable SEQRES records for 1GXC.pdbqt (#1) chain E; guessing termini instead
1057No usable SEQRES records for 1GXC.pdbqt (#1) chain G; guessing termini instead
10583 messages similar to the above omitted
1059Chain-initial residues that are actual N termini: /A PRO 92, /B HIS 0, /D PRO
106092, /E HIS 0, /G PRO 92, /H HIS 0, /J PRO 92, /K HIS 0
1061Chain-initial residues that are not actual N termini: /B TYR 4, /E TYR 4, /H
1062TYR 4, /K TYR 4
1063Chain-final residues that are actual C termini: /A ASP 207, /B ARG 7, /D ASP
1064207, /E ARG 7, /G ASP 207, /H ARG 7, /J ASP 207, /K ARG 7
1065Chain-final residues that are not actual C termini: /B ASP 2, /E ASP 2, /H ASP
10662, /K ASP 2
1067388 hydrogen bonds
1068Adding 'H' to /B TYR 4
1069Adding 'H' to /E TYR 4
1070Adding 'H' to /H TYR 4
1071Adding 'H' to /K TYR 4
1072/B ASP 2 is not terminus, removing H atom from 'C'
1073/E ASP 2 is not terminus, removing H atom from 'C'
1074/H ASP 2 is not terminus, removing H atom from 'C'
1075/K ASP 2 is not terminus, removing H atom from 'C'
10760 hydrogens added
1077
1078
1079> wait 5
1080
1081> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1GXC--
1082> WRM-16.result.pdbqt
1083
1084Summary of feedback from opening
1085/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1GXC--WRM-16.result.pdbqt
1086---
1087warnings | Ignored bad PDB record found on line 2
1088REMARK VINA RESULT: -7.0 0.000 0.000
1089
1090Ignored bad PDB record found on line 3
1091REMARK 5 active torsions:
1092
1093Ignored bad PDB record found on line 4
1094REMARK status: ('A' for Active; 'I' for Inactive)
1095
1096Ignored bad PDB record found on line 5
1097REMARK 1 A between atoms: C_9 and O_15
1098
1099Ignored bad PDB record found on line 6
1100REMARK 2 A between atoms: C_10 and O_17
1101
1102184 messages similar to the above omitted
1103
1104Opened 1GXC--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
1105bonds)
1106
1107> wait 5
1108
1109> close #2.2-9
1110
1111> wait 5
1112
1113> contacts :UNL radius 0.05 log true saveFile
1114> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
1115> WRM-16.contacts.txt
1116
1117
1118 Allowed overlap: -0.4
1119 H-bond overlap reduction: 0.4
1120 Ignore contacts between atoms separated by 4 bonds or less
1121 Detect intra-residue contacts: False
1122 Detect intra-molecule contacts: True
1123
1124 30 contacts
1125 atom1 atom2 overlap distance
1126 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 184 HB2 0.193 2.567
1127 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 HA 0.144 2.736
1128 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 3HD1 0.103 2.657
1129 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 HN 0.074 2.806
1130 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 HB2 0.014 2.866
1131 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 HA -0.111 2.721
1132 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 CB -0.140 3.720
1133 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CA -0.141 3.721
1134 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 186 O -0.141 3.381
1135 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 3HD1 -0.151 2.761
1136 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G ARG 132 HD1 -0.159 2.619
1137 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 O -0.179 3.539
1138 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 184 CB -0.181 3.641
1139 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 N -0.199 3.584
1140 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 HB2 -0.204 2.964
1141 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G LEU 129 HA -0.211 2.631
1142 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 O -0.218 3.458
1143 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G ARG 132 CD -0.232 3.392
1144 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 186 HB1 -0.235 2.995
1145 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G LEU 129 O -0.252 3.152
1146 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 HN -0.264 3.024
1147 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CD1 -0.264 3.724
1148 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 N -0.278 3.783
1149 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 3HD1 -0.301 3.061
1150 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 HB1 -0.310 3.070
1151 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 N -0.338 3.843
1152 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CD1 -0.354 3.664
1153 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G ARG 132 HD1 -0.355 3.235
1154 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/D ASN 186 HB2 -0.377 2.837
1155 1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CD1 -0.396 3.856
1156
1157
1158
115930 contacts
1160
1161> hbonds :UNL showDist true radius 0.05 log true saveFile
1162> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
1163> WRM-16.hbonds.txt
1164
1165
1166 Finding intermodel H-bonds
1167 Finding intramodel H-bonds
1168 Constraints relaxed by 0.4 angstroms and 20 degrees
1169 Models used:
1170 1 1GXC.pdbqt
1171 2.1 1GXC--WRM-16.result.pdbqt
1172
1173 0 H-bonds
1174 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1175
1176
1177
11780 hydrogen bonds found
1179
1180> select :UNL
1181
118228 atoms, 31 bonds, 1 residue, 1 model selected
1183
1184> label sel text "Ligand "
1185
1186> label height 1
1187
1188> ~select
1189
1190Nothing selected
1191
1192> 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03
1193> ypos .95
1194
1195> 2dlabels text "1GXC WRM-16 Complex" color gray size 18 xpos .03 ypos .91
1196
1197> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
1198> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
1199> true
1200
1201> select :UNL
1202
120328 atoms, 31 bonds, 1 residue, 1 model selected
1204
1205> view sel
1206
1207> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
1208> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
1209> true
1210
1211> close
1212
1213> wait 5
1214
1215> set bgColor white
1216
1217> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1KO6.pdbqt
1218
1219Chain information for 1KO6.pdbqt #1
1220---
1221Chain | Description
1222A | No description available
1223B D | No description available
1224C | No description available
1225
1226Opened 1KO6.pdbqt containing 1 structures (4955 atoms, 5004 bonds)
1227
1228> wait 5
1229
1230> hide surfaces
1231
1232> hide atoms
1233
1234> show cartoons
1235
1236> wait 5
1237
1238> addh
1239
1240Summary of feedback from adding hydrogens to 1KO6.pdbqt #1
1241---
1242warnings | Not adding hydrogens to /A MET 712 CB because it is missing heavy-
1243atom bond partners
1244Not adding hydrogens to /A LYS 814 CB because it is missing heavy-atom bond
1245partners
1246Not adding hydrogens to /C THR 737 CB because it is missing heavy-atom bond
1247partners
1248Not adding hydrogens to /D ASP 870 CB because it is missing heavy-atom bond
1249partners
1250notes | No usable SEQRES records for 1KO6.pdbqt (#1) chain A; guessing termini
1251instead
1252No usable SEQRES records for 1KO6.pdbqt (#1) chain B; guessing termini instead
1253No usable SEQRES records for 1KO6.pdbqt (#1) chain C; guessing termini instead
1254No usable SEQRES records for 1KO6.pdbqt (#1) chain D; guessing termini instead
1255Chain-initial residues that are actual N termini: /A MET 712, /B LYS 865, /C
1256HIS 713, /D LYS 865
1257Chain-initial residues that are not actual N termini: /C GLU 742
1258Chain-final residues that are actual C termini: /A PHE 863, /B ASP 870, /C PHE
1259863, /D ASP 870
1260Chain-final residues that are not actual C termini: /C ASN 738
1261223 hydrogen bonds
1262Adding 'H' to /C GLU 742
1263/C ASN 738 is not terminus, removing H atom from 'C'
12641 hydrogens added
1265
1266
1267> wait 5
1268
1269> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1KO6--
1270> WRM-16.result.pdbqt
1271
1272Summary of feedback from opening
1273/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1KO6--WRM-16.result.pdbqt
1274---
1275warnings | Ignored bad PDB record found on line 2
1276REMARK VINA RESULT: -7.3 0.000 0.000
1277
1278Ignored bad PDB record found on line 3
1279REMARK 5 active torsions:
1280
1281Ignored bad PDB record found on line 4
1282REMARK status: ('A' for Active; 'I' for Inactive)
1283
1284Ignored bad PDB record found on line 5
1285REMARK 1 A between atoms: C_9 and O_15
1286
1287Ignored bad PDB record found on line 6
1288REMARK 2 A between atoms: C_10 and O_17
1289
1290184 messages similar to the above omitted
1291
1292Opened 1KO6--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
1293bonds)
1294
1295> wait 5
1296
1297> close #2.2-9
1298
1299> wait 5
1300
1301> contacts :UNL radius 0.05 log true saveFile
1302> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
1303> WRM-16.contacts.txt
1304
1305
1306 Allowed overlap: -0.4
1307 H-bond overlap reduction: 0.4
1308 Ignore contacts between atoms separated by 4 bonds or less
1309 Detect intra-residue contacts: False
1310 Detect intra-molecule contacts: True
1311
1312 36 contacts
1313 atom1 atom2 overlap distance
1314 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 3HD2 0.149 2.461
1315 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 3HD2 0.075 2.535
1316 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 HB2 0.038 2.722
1317 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 HB2 0.022 2.738
1318 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 3HD2 -0.109 2.869
1319 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A VAL 783 2HG1 -0.121 2.731
1320 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 NH2 -0.144 3.649
1321 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CD2 -0.149 3.459
1322 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 CE1 -0.153 3.613
1323 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 HD1 -0.165 2.925
1324 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 C -0.168 3.628
1325 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/C GLU 848 OE2 -0.172 3.412
1326 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 HD1 -0.179 2.939
1327 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 CZ -0.190 3.770
1328 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 CZ -0.200 3.780
1329 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 1KO6.pdbqt #1/A ARG 778 CZ -0.201 3.361
1330 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 1KO6.pdbqt #1/A LEU 786 3HD2 -0.234 2.694
1331 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 ND1 -0.236 3.621
1332 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CD2 -0.243 3.553
1333 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 HE1 -0.244 3.004
1334 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 C -0.255 3.715
1335 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 NE -0.258 3.763
1336 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 N -0.265 3.650
1337 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 1KO6.pdbqt #1/A ARG 778 CZ -0.299 3.419
1338 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 ND1 -0.302 3.687
1339 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 HB2 -0.308 3.068
1340 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 HB2 -0.317 3.077
1341 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/C ARG 850 HD1 -0.328 3.088
1342 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/C ARG 850 CD -0.334 3.794
1343 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 CE1 -0.338 3.798
1344 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 CB -0.340 3.800
1345 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CB -0.345 3.805
1346 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 O -0.353 3.593
1347 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A VAL 783 CG1 -0.358 3.668
1348 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CB -0.362 3.822
1349 1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 HB2 -0.365 3.125
1350
1351
1352
135336 contacts
1354
1355> hbonds :UNL showDist true radius 0.05 log true saveFile
1356> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
1357> WRM-16.hbonds.txt
1358
1359
1360 Finding intermodel H-bonds
1361 Finding intramodel H-bonds
1362 Constraints relaxed by 0.4 angstroms and 20 degrees
1363 Models used:
1364 1 1KO6.pdbqt
1365 2.1 1KO6--WRM-16.result.pdbqt
1366
1367 0 H-bonds
1368 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1369
1370
1371
13720 hydrogen bonds found
1373
1374> select :UNL
1375
137628 atoms, 31 bonds, 1 residue, 1 model selected
1377
1378> label sel text "Ligand "
1379
1380> label height 1
1381
1382> ~select
1383
1384Nothing selected
1385
1386> 2dlabels text "Binding Energy: -7.3 kcal/mol" color red size 18 xpos .03
1387> ypos .95
1388
1389> 2dlabels text "1KO6 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
1390
1391> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
1392> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
1393> true
1394
1395> select :UNL
1396
139728 atoms, 31 bonds, 1 residue, 1 model selected
1398
1399> view sel
1400
1401> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
1402> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
1403> true
1404
1405> close
1406
1407> wait 5
1408
1409> set bgColor white
1410
1411> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2I2Y.pdbqt
1412
1413Chain information for 2I2Y.pdbqt #1
1414---
1415Chain | Description
1416A | No description available
1417B | No description available
1418
1419Opened 2I2Y.pdbqt containing 1 structures (2441 atoms, 2472 bonds)
1420
1421> wait 5
1422
1423> hide surfaces
1424
1425> hide atoms
1426
1427> show cartoons
1428
1429> wait 5
1430
1431> addh
1432
1433Summary of feedback from adding hydrogens to 2I2Y.pdbqt #1
1434---
1435notes | No usable SEQRES records for 2I2Y.pdbqt (#1) chain A; guessing termini
1436instead
1437No usable SEQRES records for 2I2Y.pdbqt (#1) chain B; guessing termini instead
1438Chain-initial residues that are actual N termini: /A MET 1, /B C 151
1439Chain-initial residues that are not actual N termini:
1440Chain-final residues that are actual C termini: /A ARG 150, /B C 154
1441Chain-final residues that are not actual C termini:
1442171 hydrogen bonds
144310 hydrogens added
1444
1445
1446> wait 5
1447
1448> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2I2Y--
1449> WRM-16.result.pdbqt
1450
1451Summary of feedback from opening
1452/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2I2Y--WRM-16.result.pdbqt
1453---
1454warnings | Ignored bad PDB record found on line 2
1455REMARK VINA RESULT: -6.7 0.000 0.000
1456
1457Ignored bad PDB record found on line 3
1458REMARK 5 active torsions:
1459
1460Ignored bad PDB record found on line 4
1461REMARK status: ('A' for Active; 'I' for Inactive)
1462
1463Ignored bad PDB record found on line 5
1464REMARK 1 A between atoms: C_9 and O_15
1465
1466Ignored bad PDB record found on line 6
1467REMARK 2 A between atoms: C_10 and O_17
1468
1469184 messages similar to the above omitted
1470
1471Opened 2I2Y--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
1472bonds)
1473
1474> wait 5
1475
1476> close #2.2-9
1477
1478> wait 5
1479
1480> contacts :UNL radius 0.05 log true saveFile
1481> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
1482> WRM-16.contacts.txt
1483
1484
1485 Allowed overlap: -0.4
1486 H-bond overlap reduction: 0.4
1487 Ignore contacts between atoms separated by 4 bonds or less
1488 Detect intra-residue contacts: False
1489 Detect intra-molecule contacts: True
1490
1491 42 contacts
1492 atom1 atom2 overlap distance
1493 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 O 0.082 3.158
1494 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 0.042 2.568
1495 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD1 0.038 2.722
1496 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 0.018 2.592
1497 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 0.002 2.608
1498 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 -0.056 2.936
1499 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HA -0.087 2.847
1500 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ARG 128 HG2 -0.102 2.862
1501 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD1 -0.104 2.864
1502 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 N -0.108 3.613
1503 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 -0.117 2.877
1504 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 O 2I2Y.pdbqt #1/A ASP 73 O -0.129 3.029
1505 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HA -0.132 3.012
1506 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD2 -0.137 3.717
1507 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CA -0.151 3.731
1508 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HB3 -0.156 2.916
1509 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 -0.160 2.920
1510 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 OD1 -0.177 3.417
1511 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HB3 -0.188 2.798
1512 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CB -0.194 3.504
1513 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 123 C -0.215 3.795
1514 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2I2Y.pdbqt #1/A ARG 150 CZ -0.217 3.797
1515 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2I2Y.pdbqt #1/A ARG 150 NH1 -0.264 3.769
1516 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CB -0.268 3.578
1517 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 -0.274 3.034
1518 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD1 -0.276 3.736
1519 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CB -0.297 3.877
1520 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A VAL 127 CG1 -0.301 3.761
1521 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD2 -0.306 3.616
1522 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A VAL 127 CG1 -0.313 3.773
1523 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 -0.320 2.930
1524 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2I2Y.pdbqt #1/A ARG 150 NH2 -0.323 3.828
1525 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ARG 128 HG2 -0.332 3.092
1526 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 68 O -0.337 3.577
1527 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 CB -0.338 3.648
1528 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 123 CB -0.338 3.918
1529 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ARG 128 CG -0.343 3.803
1530 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 O 2I2Y.pdbqt #1/A SER 69 OG -0.346 2.866
1531 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CA -0.358 3.818
1532 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A SER 69 OG -0.359 3.469
1533 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD2 -0.367 3.677
1534 2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 123 HB2 -0.389 3.269
1535
1536
1537
153842 contacts
1539
1540> hbonds :UNL showDist true radius 0.05 log true saveFile
1541> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
1542> WRM-16.hbonds.txt
1543
1544
1545 Finding intermodel H-bonds
1546 Finding intramodel H-bonds
1547 Constraints relaxed by 0.4 angstroms and 20 degrees
1548 Models used:
1549 1 2I2Y.pdbqt
1550 2.1 2I2Y--WRM-16.result.pdbqt
1551
1552 0 H-bonds
1553 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1554
1555
1556
15570 hydrogen bonds found
1558
1559> select :UNL
1560
156128 atoms, 31 bonds, 1 residue, 1 model selected
1562
1563> label sel text "Ligand "
1564
1565> label height 1
1566
1567> ~select
1568
1569Nothing selected
1570
1571> 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
1572> ypos .95
1573
1574> 2dlabels text "2I2Y WRM-16 Complex" color gray size 18 xpos .03 ypos .91
1575
1576> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
1577> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
1578> true
1579
1580> select :UNL
1581
158228 atoms, 31 bonds, 1 residue, 1 model selected
1583
1584> view sel
1585
1586> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
1587> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
1588> true
1589
1590> close
1591
1592> wait 5
1593
1594> set bgColor white
1595
1596> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2CPE.pdbqt
1597
1598Chain information for 2CPE.pdbqt #1
1599---
1600Chain | Description
1601A | No description available
1602
1603Opened 2CPE.pdbqt containing 1 structures (1663 atoms, 1680 bonds)
1604
1605> wait 5
1606
1607> hide surfaces
1608
1609> hide atoms
1610
1611> show cartoons
1612
1613> wait 5
1614
1615> addh
1616
1617Summary of feedback from adding hydrogens to 2CPE.pdbqt #1
1618---
1619notes | No usable SEQRES records for 2CPE.pdbqt (#1) chain A; guessing termini
1620instead
1621Chain-initial residues that are actual N termini: /A GLY 346
1622Chain-initial residues that are not actual N termini:
1623Chain-final residues that are actual C termini: /A GLY 458
1624Chain-final residues that are not actual C termini:
162543 hydrogen bonds
16261 hydrogens added
1627
1628
1629> wait 5
1630
1631> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CPE--
1632> WRM-16.result.pdbqt
1633
1634Summary of feedback from opening
1635/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CPE--WRM-16.result.pdbqt
1636---
1637warnings | Ignored bad PDB record found on line 2
1638REMARK VINA RESULT: -6.4 0.000 0.000
1639
1640Ignored bad PDB record found on line 3
1641REMARK 5 active torsions:
1642
1643Ignored bad PDB record found on line 4
1644REMARK status: ('A' for Active; 'I' for Inactive)
1645
1646Ignored bad PDB record found on line 5
1647REMARK 1 A between atoms: C_9 and O_15
1648
1649Ignored bad PDB record found on line 6
1650REMARK 2 A between atoms: C_10 and O_17
1651
1652184 messages similar to the above omitted
1653
1654Opened 2CPE--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
1655bonds)
1656
1657> wait 5
1658
1659> close #2.2-9
1660
1661> wait 5
1662
1663> contacts :UNL radius 0.05 log true saveFile
1664> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
1665> WRM-16.contacts.txt
1666
1667
1668 Allowed overlap: -0.4
1669 H-bond overlap reduction: 0.4
1670 Ignore contacts between atoms separated by 4 bonds or less
1671 Detect intra-residue contacts: False
1672 Detect intra-molecule contacts: True
1673
1674 45 contacts
1675 atom1 atom2 overlap distance
1676 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 374 HB2 0.239 2.521
1677 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A ILE 400 H 0.104 2.776
1678 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB 0.090 2.670
1679 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A VAL 372 O 0.010 2.930
1680 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.008 2.768
1681 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A HIS 399 ND1 -0.011 3.516
1682 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 O -0.023 3.263
1683 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CD1 -0.043 3.503
1684 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A THR 373 2HG2 -0.051 2.511
1685 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A HIS 399 CE1 -0.060 3.640
1686 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 374 CB -0.065 3.525
1687 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.072 2.832
1688 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.104 2.714
1689 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 374 H -0.106 2.126
1690 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 2HD2 -0.122 3.002
1691 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.144 2.754
1692 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 3HD1 -0.145 2.755
1693 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A VAL 372 O -0.165 3.525
1694 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 CD1 -0.165 3.625
1695 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A GLY 407 O -0.173 3.413
1696 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.190 2.800
1697 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 402 3HD1 -0.198 2.658
1698 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A ILE 400 N -0.226 3.731
1699 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.233 2.993
1700 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CB -0.257 3.717
1701 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.296 3.176
1702 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 CD1 -0.306 3.766
1703 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A HIS 399 HA -0.312 3.192
1704 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.326 3.086
1705 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A THR 373 2HG2 -0.326 3.206
1706 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A THR 373 HA -0.326 2.746
1707 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 H -0.328 2.938
1708 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A THR 373 HA -0.343 3.223
1709 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CB -0.348 3.808
1710 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CG1 -0.351 3.811
1711 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.367 2.977
1712 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 374 HB2 -0.373 3.133
1713 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A THR 373 CG2 -0.376 3.536
1714 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A ASP 370 O -0.382 3.282
1715 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 1HD1 -0.384 3.144
1716 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 374 N -0.385 3.030
1717 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CB -0.390 3.850
1718 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A GLY 407 O -0.392 3.632
1719 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CD1 -0.398 3.708
1720 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 CD1 -0.400 3.710
1721
1722
1723
172445 contacts
1725
1726> hbonds :UNL showDist true radius 0.05 log true saveFile
1727> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
1728> WRM-16.hbonds.txt
1729
1730
1731 Finding intermodel H-bonds
1732 Finding intramodel H-bonds
1733 Constraints relaxed by 0.4 angstroms and 20 degrees
1734 Models used:
1735 1 2CPE.pdbqt
1736 2.1 2CPE--WRM-16.result.pdbqt
1737
1738 1 H-bonds
1739 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1740 2CPE.pdbqt #1/A LEU 374 N 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 374 H 3.030 2.126
1741
1742
1743
17441 hydrogen bonds found
1745
1746> select :UNL
1747
174828 atoms, 31 bonds, 1 residue, 1 model selected
1749
1750> label sel text "Ligand "
1751
1752> label height 1
1753
1754> ~select
1755
1756Nothing selected
1757
1758> 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03
1759> ypos .95
1760
1761> 2dlabels text "2CPE WRM-16 Complex" color gray size 18 xpos .03 ypos .91
1762
1763> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
1764> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
1765> true
1766
1767> select :UNL
1768
176928 atoms, 31 bonds, 1 residue, 1 model selected
1770
1771> view sel
1772
1773> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
1774> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
1775> true
1776
1777> close
1778
1779> wait 5
1780
1781> set bgColor white
1782
1783> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XQZ.pdbqt
1784
1785Chain information for 1XQZ.pdbqt #1
1786---
1787Chain | Description
1788A | No description available
1789
1790Opened 1XQZ.pdbqt containing 1 structures (4460 atoms, 4520 bonds)
1791
1792> wait 5
1793
1794> hide surfaces
1795
1796> hide atoms
1797
1798> show cartoons
1799
1800> wait 5
1801
1802> addh
1803
1804Summary of feedback from adding hydrogens to 1XQZ.pdbqt #1
1805---
1806notes | No usable SEQRES records for 1XQZ.pdbqt (#1) chain A; guessing termini
1807instead
1808Chain-initial residues that are actual N termini: /A GLU 32
1809Chain-initial residues that are not actual N termini:
1810Chain-final residues that are actual C termini: /A SER 308
1811Chain-final residues that are not actual C termini:
1812219 hydrogen bonds
18135 hydrogens added
1814
1815
1816> wait 5
1817
1818> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XQZ--
1819> WRM-16.result.pdbqt
1820
1821Summary of feedback from opening
1822/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XQZ--WRM-16.result.pdbqt
1823---
1824warnings | Ignored bad PDB record found on line 2
1825REMARK VINA RESULT: -9.1 0.000 0.000
1826
1827Ignored bad PDB record found on line 3
1828REMARK 5 active torsions:
1829
1830Ignored bad PDB record found on line 4
1831REMARK status: ('A' for Active; 'I' for Inactive)
1832
1833Ignored bad PDB record found on line 5
1834REMARK 1 A between atoms: C_9 and O_15
1835
1836Ignored bad PDB record found on line 6
1837REMARK 2 A between atoms: C_10 and O_17
1838
1839184 messages similar to the above omitted
1840
1841Opened 1XQZ--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
1842bonds)
1843
1844> wait 5
1845
1846> close #2.2-9
1847
1848> wait 5
1849
1850> contacts :UNL radius 0.05 log true saveFile
1851> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
1852> WRM-16.contacts.txt
1853
1854
1855 Allowed overlap: -0.4
1856 H-bond overlap reduction: 0.4
1857 Ignore contacts between atoms separated by 4 bonds or less
1858 Detect intra-residue contacts: False
1859 Detect intra-molecule contacts: True
1860
1861 84 contacts
1862 atom1 atom2 overlap distance
1863 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 0.680 2.080
1864 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 0.609 2.151
1865 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 2HG1 0.394 2.366
1866 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD1 0.391 3.069
1867 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HN 0.374 2.386
1868 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HB1 0.366 2.514
1869 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD1 0.197 3.263
1870 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CE1 0.188 3.392
1871 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 3HG1 0.163 2.597
1872 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 2HG1 0.161 2.599
1873 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 N 0.156 3.229
1874 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LYS 67 HZ3 0.141 2.619
1875 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ARG 122 HG1 0.131 2.289
1876 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 3HD1 0.128 2.752
1877 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CG1 0.076 3.384
1878 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 44 3HD1 0.076 2.684
1879 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A GLU 121 O 0.067 3.293
1880 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HN 0.067 2.693
1881 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 0.066 2.694
1882 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A LEU 174 1HD1 0.058 2.402
1883 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CB 0.050 3.530
1884 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CZ 0.039 3.541
1885 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 2HD2 0.018 2.742
1886 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HN -0.011 2.771
1887 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ALA 65 CB -0.021 3.601
1888 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HA -0.021 2.781
1889 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CG1 -0.024 3.484
1890 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD1 -0.026 3.486
1891 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 1HG2 -0.033 2.913
1892 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ILE 104 1HG2 -0.053 2.513
1893 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 N -0.056 3.441
1894 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CA -0.060 3.520
1895 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 3HG1 -0.062 2.822
1896 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CD1 -0.070 3.650
1897 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD2 -0.091 3.551
1898 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 HB -0.091 2.701
1899 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 CG1 -0.109 3.569
1900 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LYS 67 NZ -0.112 3.497
1901 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A PHE 49 CE1 -0.120 3.280
1902 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CA -0.125 3.585
1903 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 HB -0.127 2.887
1904 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 174 1HD1 -0.155 3.035
1905 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 3HD1 -0.155 2.765
1906 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HA -0.161 2.921
1907 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 CG1 -0.171 3.631
1908 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CD1 -0.174 3.634
1909 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CG2 -0.176 3.636
1910 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ARG 122 CG -0.191 3.311
1911 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CD1 -0.193 3.773
1912 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ALA 65 HB3 -0.203 3.083
1913 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 3HG1 -0.203 2.813
1914 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A LEU 174 CD1 -0.209 3.369
1915 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 -0.219 2.829
1916 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LYS 67 HD1 -0.229 2.989
1917 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 3HD1 -0.241 2.851
1918 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CB -0.253 3.713
1919 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 HB -0.285 2.895
1920 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CG2 -0.295 3.605
1921 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 2HG2 -0.296 2.906
1922 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1XQZ.pdbqt #1/A VAL 126 O -0.301 3.661
1923 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CB -0.302 3.612
1924 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CG -0.304 3.884
1925 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CG2 -0.306 3.886
1926 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A VAL 52 1HG1 -0.309 2.769
1927 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 N -0.313 3.698
1928 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 2HD1 -0.313 3.073
1929 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ARG 122 HD2 -0.324 3.084
1930 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 52 1HG1 -0.325 2.935
1931 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 44 CD1 -0.326 3.786
1932 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ILE 185 2HG2 -0.327 2.787
1933 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 174 1HD2 -0.328 3.208
1934 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 1HG2 -0.336 3.096
1935 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CD1 -0.337 3.647
1936 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CE2 -0.340 3.920
1937 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CG2 -0.342 3.652
1938 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 2HD1 -0.346 3.106
1939 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 52 1HG2 -0.351 2.961
1940 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CG -0.363 3.823
1941 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 1HG2 -0.366 3.126
1942 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ILE 185 CG2 -0.373 3.533
1943 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CB -0.387 3.967
1944 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 HB2 -0.393 3.273
1945 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CB -0.393 3.853
1946 1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 CG2 -0.396 3.856
1947
1948
1949
195084 contacts
1951
1952> hbonds :UNL showDist true radius 0.05 log true saveFile
1953> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
1954> WRM-16.hbonds.txt
1955
1956
1957 Finding intermodel H-bonds
1958 Finding intramodel H-bonds
1959 Constraints relaxed by 0.4 angstroms and 20 degrees
1960 Models used:
1961 1 1XQZ.pdbqt
1962 2.1 1XQZ--WRM-16.result.pdbqt
1963
1964 0 H-bonds
1965 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1966
1967
1968
19690 hydrogen bonds found
1970
1971> select :UNL
1972
197328 atoms, 31 bonds, 1 residue, 1 model selected
1974
1975> label sel text "Ligand "
1976
1977> label height 1
1978
1979> ~select
1980
1981Nothing selected
1982
1983> 2dlabels text "Binding Energy: -9.1 kcal/mol" color red size 18 xpos .03
1984> ypos .95
1985
1986> 2dlabels text "1XQZ WRM-16 Complex" color gray size 18 xpos .03 ypos .91
1987
1988> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
1989> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
1990> true
1991
1992> select :UNL
1993
199428 atoms, 31 bonds, 1 residue, 1 model selected
1995
1996> view sel
1997
1998> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
1999> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
2000> true
2001
2002> close
2003
2004> wait 5
2005
2006> set bgColor white
2007
2008> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1Z00.pdbqt
2009
2010Chain information for 1Z00.pdbqt #1
2011---
2012Chain | Description
2013A | No description available
2014B | No description available
2015
2016Opened 1Z00.pdbqt containing 1 structures (2620 atoms, 2640 bonds)
2017
2018> wait 5
2019
2020> hide surfaces
2021
2022> hide atoms
2023
2024> show cartoons
2025
2026> wait 5
2027
2028> addh
2029
2030Summary of feedback from adding hydrogens to 1Z00.pdbqt #1
2031---
2032notes | No usable SEQRES records for 1Z00.pdbqt (#1) chain A; guessing termini
2033instead
2034No usable SEQRES records for 1Z00.pdbqt (#1) chain B; guessing termini instead
2035Chain-initial residues that are actual N termini: /A MET 219, /B MET 822
2036Chain-initial residues that are not actual N termini:
2037Chain-final residues that are actual C termini: /A HIS 302, /B LYS 905
2038Chain-final residues that are not actual C termini:
2039131 hydrogen bonds
20400 hydrogens added
2041
2042
2043> wait 5
2044
2045> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1Z00--
2046> WRM-16.result.pdbqt
2047
2048Summary of feedback from opening
2049/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1Z00--WRM-16.result.pdbqt
2050---
2051warnings | Ignored bad PDB record found on line 2
2052REMARK VINA RESULT: -6.8 0.000 0.000
2053
2054Ignored bad PDB record found on line 3
2055REMARK 5 active torsions:
2056
2057Ignored bad PDB record found on line 4
2058REMARK status: ('A' for Active; 'I' for Inactive)
2059
2060Ignored bad PDB record found on line 5
2061REMARK 1 A between atoms: C_9 and O_15
2062
2063Ignored bad PDB record found on line 6
2064REMARK 2 A between atoms: C_10 and O_17
2065
2066184 messages similar to the above omitted
2067
2068Opened 1Z00--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
2069bonds)
2070
2071> wait 5
2072
2073> close #2.2-9
2074
2075> wait 5
2076
2077> contacts :UNL radius 0.05 log true saveFile
2078> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
2079> WRM-16.contacts.txt
2080
2081
2082 Allowed overlap: -0.4
2083 H-bond overlap reduction: 0.4
2084 Ignore contacts between atoms separated by 4 bonds or less
2085 Detect intra-residue contacts: False
2086 Detect intra-molecule contacts: True
2087
2088 52 contacts
2089 atom1 atom2 overlap distance
2090 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 HB2 0.383 2.377
2091 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 222 3HD2 0.372 2.388
2092 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 CB 0.368 3.092
2093 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 HA 0.193 2.687
2094 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 O 0.163 3.197
2095 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB3 0.104 2.656
2096 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 HB3 0.064 2.696
2097 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 CB 0.063 3.397
2098 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 222 CD2 0.020 3.440
2099 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB 0.011 3.449
2100 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 CD1 -0.010 3.470
2101 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 CA -0.022 3.602
2102 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB -0.036 3.496
2103 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HA -0.039 2.649
2104 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HZ3 -0.040 2.800
2105 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HZ3 -0.042 2.802
2106 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB3 -0.083 2.843
2107 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 HB2 -0.087 2.507
2108 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 HB2 -0.092 2.852
2109 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HB2 -0.100 2.860
2110 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 HB3 -0.122 2.882
2111 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 3HD1 -0.124 2.884
2112 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ASP 230 OD2 -0.127 3.367
2113 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 HB3 -0.147 2.907
2114 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 CB -0.189 3.349
2115 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 O -0.208 3.568
2116 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 CB -0.211 3.671
2117 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HA -0.218 2.828
2118 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 CD -0.225 3.685
2119 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB -0.228 3.688
2120 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB1 -0.260 3.020
2121 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 NZ -0.264 3.649
2122 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 CB -0.269 3.729
2123 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/B GLN 885 OE1 -0.287 3.227
2124 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 CD1 -0.288 3.868
2125 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HB3 -0.291 3.051
2126 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1Z00.pdbqt #1/A LEU 222 CD2 -0.295 3.875
2127 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB -0.302 3.762
2128 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A MET 219 O -0.310 3.400
2129 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB3 -0.324 3.084
2130 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HA -0.326 3.086
2131 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 CG -0.329 3.489
2132 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 NZ -0.336 3.721
2133 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 N -0.340 3.845
2134 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CA -0.348 3.658
2135 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 HB3 -0.357 2.817
2136 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 CB -0.359 3.819
2137 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 CB -0.362 3.822
2138 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 CB -0.369 3.829
2139 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ASP 230 OD2 -0.371 3.461
2140 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ASP 230 OD2 -0.380 3.470
2141 1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 CB -0.386 3.506
2142
2143
2144
214552 contacts
2146
2147> hbonds :UNL showDist true radius 0.05 log true saveFile
2148> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
2149> WRM-16.hbonds.txt
2150
2151
2152 Finding intermodel H-bonds
2153 Finding intramodel H-bonds
2154 Constraints relaxed by 0.4 angstroms and 20 degrees
2155 Models used:
2156 1 1Z00.pdbqt
2157 2.1 1Z00--WRM-16.result.pdbqt
2158
2159 0 H-bonds
2160 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2161
2162
2163
21640 hydrogen bonds found
2165
2166> select :UNL
2167
216828 atoms, 31 bonds, 1 residue, 1 model selected
2169
2170> label sel text "Ligand "
2171
2172> label height 1
2173
2174> ~select
2175
2176Nothing selected
2177
2178> 2dlabels text "Binding Energy: -6.8 kcal/mol" color red size 18 xpos .03
2179> ypos .95
2180
2181> 2dlabels text "1Z00 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
2182
2183> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
2184> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
2185> true
2186
2187> select :UNL
2188
218928 atoms, 31 bonds, 1 residue, 1 model selected
2190
2191> view sel
2192
2193> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
2194> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
2195> true
2196
2197> close
2198
2199> wait 5
2200
2201> set bgColor white
2202
2203> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2N1I.pdbqt
2204
2205Chain information for 2N1I.pdbqt #1
2206---
2207Chain | Description
2208A | No description available
2209
2210Opened 2N1I.pdbqt containing 1 structures (2650 atoms, 2682 bonds)
2211
2212> wait 5
2213
2214> hide surfaces
2215
2216> hide atoms
2217
2218> show cartoons
2219
2220> wait 5
2221
2222> addh
2223
2224Summary of feedback from adding hydrogens to 2N1I.pdbqt #1
2225---
2226notes | No usable SEQRES records for 2N1I.pdbqt (#1) chain A; guessing termini
2227instead
2228Chain-initial residues that are actual N termini: /A GLY 51
2229Chain-initial residues that are not actual N termini:
2230Chain-final residues that are actual C termini: /A GLU 226
2231Chain-final residues that are not actual C termini:
223270 hydrogen bonds
22330 hydrogens added
2234
2235
2236> wait 5
2237
2238> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2N1I--
2239> WRM-16.result.pdbqt
2240
2241Summary of feedback from opening
2242/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2N1I--WRM-16.result.pdbqt
2243---
2244warnings | Ignored bad PDB record found on line 2
2245REMARK VINA RESULT: -6.7 0.000 0.000
2246
2247Ignored bad PDB record found on line 3
2248REMARK 5 active torsions:
2249
2250Ignored bad PDB record found on line 4
2251REMARK status: ('A' for Active; 'I' for Inactive)
2252
2253Ignored bad PDB record found on line 5
2254REMARK 1 A between atoms: C_9 and O_15
2255
2256Ignored bad PDB record found on line 6
2257REMARK 2 A between atoms: C_10 and O_17
2258
2259184 messages similar to the above omitted
2260
2261Opened 2N1I--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
2262bonds)
2263
2264> wait 5
2265
2266> close #2.2-9
2267
2268> wait 5
2269
2270> contacts :UNL radius 0.05 log true saveFile
2271> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
2272> WRM-16.contacts.txt
2273
2274
2275 Allowed overlap: -0.4
2276 H-bond overlap reduction: 0.4
2277 Ignore contacts between atoms separated by 4 bonds or less
2278 Detect intra-residue contacts: False
2279 Detect intra-molecule contacts: True
2280
2281 54 contacts
2282 atom1 atom2 overlap distance
2283 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 H 0.318 2.562
2284 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 0.108 2.652
2285 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 HB3 0.091 2.789
2286 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 3HG1 0.063 2.547
2287 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A LYS 103 O 0.016 3.344
2288 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 0.000 2.760
2289 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 3HG1 -0.025 2.635
2290 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 N -0.031 3.536
2291 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 HA -0.034 2.794
2292 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 3HG1 -0.037 2.797
2293 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A ARG 102 NH2 -0.075 3.580
2294 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CB -0.088 3.548
2295 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 H -0.095 2.975
2296 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 102 NH1 -0.100 3.605
2297 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 O -0.123 3.483
2298 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 102 2HH1 -0.129 3.009
2299 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HB2 -0.146 2.756
2300 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 83 OD1 -0.153 3.513
2301 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 CB -0.155 3.735
2302 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.170 2.780
2303 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A LYS 103 HE2 -0.171 3.051
2304 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HB3 -0.175 2.935
2305 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 CG -0.213 3.673
2306 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CG1 -0.216 3.526
2307 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A ARG 102 CZ -0.232 3.812
2308 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HA -0.236 3.116
2309 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.246 3.006
2310 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 105 H -0.256 3.016
2311 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 102 NH1 -0.256 3.641
2312 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 N -0.266 3.771
2313 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 O -0.268 3.208
2314 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 O -0.271 3.631
2315 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CA -0.275 3.855
2316 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HA -0.288 3.048
2317 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A CYS 157 O -0.304 3.544
2318 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CG1 -0.306 3.616
2319 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HB2 -0.307 3.187
2320 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A MET 104 SD -0.309 3.511
2321 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 H -0.310 2.370
2322 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CB -0.311 3.891
2323 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A MET 104 HA -0.317 3.197
2324 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CG1 -0.327 3.787
2325 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A LYS 103 CE -0.328 3.908
2326 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 CG -0.330 3.790
2327 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CA -0.338 3.798
2328 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.339 3.099
2329 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 NH1 -0.340 3.845
2330 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.369 2.979
2331 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CB -0.369 3.679
2332 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A VAL 158 CG1 -0.385 3.545
2333 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 C -0.387 3.547
2334 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HA -0.391 3.001
2335 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 83 OD2 -0.395 3.635
2336 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ARG 109 O -0.398 3.298
2337
2338
2339
234054 contacts
2341
2342> hbonds :UNL showDist true radius 0.05 log true saveFile
2343> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
2344> WRM-16.hbonds.txt
2345
2346
2347 Finding intermodel H-bonds
2348 Finding intramodel H-bonds
2349 Constraints relaxed by 0.4 angstroms and 20 degrees
2350 Models used:
2351 1 2N1I.pdbqt
2352 2.1 2N1I--WRM-16.result.pdbqt
2353
2354 1 H-bonds
2355 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2356 2N1I.pdbqt #1/A ASP 159 N 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 H 3.116 2.370
2357
2358
2359
23601 hydrogen bonds found
2361
2362> select :UNL
2363
236428 atoms, 31 bonds, 1 residue, 1 model selected
2365
2366> label sel text "Ligand "
2367
2368> label height 1
2369
2370> ~select
2371
2372Nothing selected
2373
2374> 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
2375> ypos .95
2376
2377> 2dlabels text "2N1I WRM-16 Complex" color gray size 18 xpos .03 ypos .91
2378
2379> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
2380> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
2381> true
2382
2383> select :UNL
2384
238528 atoms, 31 bonds, 1 residue, 1 model selected
2386
2387> view sel
2388
2389> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
2390> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
2391> true
2392
2393> close
2394
2395> wait 5
2396
2397> set bgColor white
2398
2399> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1P4U.pdbqt
2400
2401Chain information for 1P4U.pdbqt #1
2402---
2403Chain | Description
2404A | No description available
2405B | No description available
2406
2407Opened 1P4U.pdbqt containing 1 structures (2389 atoms, 2419 bonds)
2408
2409> wait 5
2410
2411> hide surfaces
2412
2413> hide atoms
2414
2415> show cartoons
2416
2417> wait 5
2418
2419> addh
2420
2421Summary of feedback from adding hydrogens to 1P4U.pdbqt #1
2422---
2423notes | No usable SEQRES records for 1P4U.pdbqt (#1) chain A; guessing termini
2424instead
2425No usable SEQRES records for 1P4U.pdbqt (#1) chain B; guessing termini instead
2426Chain-initial residues that are actual N termini: /A LEU 579, /B ASP -1
2427Chain-initial residues that are not actual N termini:
2428Chain-final residues that are actual C termini: /A LEU 723, /B ALA 6
2429Chain-final residues that are not actual C termini:
243095 hydrogen bonds
24311 hydrogens added
2432
2433
2434> wait 5
2435
2436> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1P4U--
2437> WRM-16.result.pdbqt
2438
2439Summary of feedback from opening
2440/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1P4U--WRM-16.result.pdbqt
2441---
2442warnings | Ignored bad PDB record found on line 2
2443REMARK VINA RESULT: -7.2 0.000 0.000
2444
2445Ignored bad PDB record found on line 3
2446REMARK 5 active torsions:
2447
2448Ignored bad PDB record found on line 4
2449REMARK status: ('A' for Active; 'I' for Inactive)
2450
2451Ignored bad PDB record found on line 5
2452REMARK 1 A between atoms: C_9 and O_15
2453
2454Ignored bad PDB record found on line 6
2455REMARK 2 A between atoms: C_10 and O_17
2456
2457184 messages similar to the above omitted
2458
2459Opened 1P4U--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
2460bonds)
2461
2462> wait 5
2463
2464> close #2.2-9
2465
2466> wait 5
2467
2468> contacts :UNL radius 0.05 log true saveFile
2469> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
2470> WRM-16.contacts.txt
2471
2472
2473 Allowed overlap: -0.4
2474 H-bond overlap reduction: 0.4
2475 Ignore contacts between atoms separated by 4 bonds or less
2476 Detect intra-residue contacts: False
2477 Detect intra-molecule contacts: True
2478
2479 55 contacts
2480 atom1 atom2 overlap distance
2481 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A THR 677 2HG2 0.351 2.409
2482 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A PRO 593 HA 0.208 2.212
2483 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ALA 614 HA 0.167 2.253
2484 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PHE 613 O 0.103 3.257
2485 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ILE 591 HB 0.100 2.320
2486 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 3HG2 0.090 2.790
2487 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD1 0.056 2.704
2488 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 HA 0.043 2.567
2489 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A THR 677 CG2 0.014 3.446
2490 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD2 -0.042 2.652
2491 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 2HG1 -0.044 2.804
2492 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A VAL 628 3HG2 -0.081 2.501
2493 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 CG2 -0.090 3.670
2494 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PHE 613 N -0.098 3.603
2495 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A SER 594 OG -0.119 3.499
2496 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HD1 -0.120 2.730
2497 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HB1 -0.124 3.004
2498 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD2 -0.157 2.917
2499 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A PRO 593 CA -0.173 3.293
2500 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HB1 -0.186 2.796
2501 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ALA 614 CA -0.187 3.307
2502 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HD1 -0.198 2.808
2503 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.204 3.439
2504 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A VAL 628 CG2 -0.210 3.370
2505 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A VAL 628 3HG2 -0.214 2.674
2506 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ILE 591 CB -0.242 3.362
2507 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A PHE 613 O -0.248 3.148
2508 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A ALA 596 O -0.255 3.615
2509 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CD2 -0.257 3.717
2510 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HD1 -0.261 3.021
2511 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 HG -0.270 3.030
2512 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD2 -0.273 3.033
2513 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.277 3.782
2514 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A LYS 592 O -0.287 3.187
2515 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 CB -0.297 3.877
2516 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 CE1 -0.299 3.879
2517 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CD1 -0.303 3.763
2518 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 3HG2 -0.306 2.916
2519 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD1 -0.312 2.922
2520 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A SER 594 HN -0.324 3.204
2521 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1P4U.pdbqt #1/A LEU 588 1HD2 -0.333 3.213
2522 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 CA -0.342 3.652
2523 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PHE 613 HN -0.343 3.223
2524 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A SER 594 HN -0.343 2.403
2525 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.350 3.735
2526 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HB1 -0.352 2.962
2527 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ILE 591 CG2 -0.367 3.527
2528 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 HA -0.370 2.980
2529 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 CA -0.376 3.956
2530 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD1 -0.379 3.139
2531 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.389 3.624
2532 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 C -0.391 3.971
2533 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CG -0.391 3.851
2534 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CD2 -0.395 3.705
2535 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 HB2 -0.395 3.005
2536
2537
2538
253955 contacts
2540
2541> hbonds :UNL showDist true radius 0.05 log true saveFile
2542> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
2543> WRM-16.hbonds.txt
2544
2545
2546 Finding intermodel H-bonds
2547 Finding intramodel H-bonds
2548 Constraints relaxed by 0.4 angstroms and 20 degrees
2549 Models used:
2550 1 1P4U.pdbqt
2551 2.1 1P4U--WRM-16.result.pdbqt
2552
2553 1 H-bonds
2554 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2555 1P4U.pdbqt #1/A SER 594 N 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A SER 594 HN 3.335 2.403
2556
2557
2558
25591 hydrogen bonds found
2560
2561> select :UNL
2562
256328 atoms, 31 bonds, 1 residue, 1 model selected
2564
2565> label sel text "Ligand "
2566
2567> label height 1
2568
2569> ~select
2570
2571Nothing selected
2572
2573> 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03
2574> ypos .95
2575
2576> 2dlabels text "1P4U WRM-16 Complex" color gray size 18 xpos .03 ypos .91
2577
2578> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
2579> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
2580> true
2581
2582> select :UNL
2583
258428 atoms, 31 bonds, 1 residue, 1 model selected
2585
2586> view sel
2587
2588> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
2589> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
2590> true
2591
2592> close
2593
2594> wait 5
2595
2596> set bgColor white
2597
2598> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KCX.pdbqt
2599
2600Chain information for 2KCX.pdbqt #1
2601---
2602Chain | Description
2603A | No description available
2604
2605Opened 2KCX.pdbqt containing 1 structures (1066 atoms, 1073 bonds)
2606
2607> wait 5
2608
2609> hide surfaces
2610
2611> hide atoms
2612
2613> show cartoons
2614
2615> wait 5
2616
2617> addh
2618
2619Summary of feedback from adding hydrogens to 2KCX.pdbqt #1
2620---
2621notes | No usable SEQRES records for 2KCX.pdbqt (#1) chain A; guessing termini
2622instead
2623Chain-initial residues that are actual N termini: /A SER 1
2624Chain-initial residues that are not actual N termini:
2625Chain-final residues that are actual C termini: /A LYS 74
2626Chain-final residues that are not actual C termini:
262756 hydrogen bonds
262810 hydrogens added
2629
2630
2631> wait 5
2632
2633> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KCX--
2634> WRM-16.result.pdbqt
2635
2636Summary of feedback from opening
2637/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KCX--WRM-16.result.pdbqt
2638---
2639warnings | Ignored bad PDB record found on line 2
2640REMARK VINA RESULT: -6.4 0.000 0.000
2641
2642Ignored bad PDB record found on line 3
2643REMARK 5 active torsions:
2644
2645Ignored bad PDB record found on line 4
2646REMARK status: ('A' for Active; 'I' for Inactive)
2647
2648Ignored bad PDB record found on line 5
2649REMARK 1 A between atoms: C_9 and O_15
2650
2651Ignored bad PDB record found on line 6
2652REMARK 2 A between atoms: C_10 and O_17
2653
2654184 messages similar to the above omitted
2655
2656Opened 2KCX--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
2657bonds)
2658
2659> wait 5
2660
2661> close #2.2-9
2662
2663> wait 5
2664
2665> contacts :UNL radius 0.05 log true saveFile
2666> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
2667> WRM-16.contacts.txt
2668
2669
2670 Allowed overlap: -0.4
2671 H-bond overlap reduction: 0.4
2672 Ignore contacts between atoms separated by 4 bonds or less
2673 Detect intra-residue contacts: False
2674 Detect intra-molecule contacts: True
2675
2676 41 contacts
2677 atom1 atom2 overlap distance
2678 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 HE2 0.106 2.504
2679 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 0.085 2.675
2680 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 0.014 2.596
2681 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 0.013 2.747
2682 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 HD3 0.006 2.874
2683 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KCX.pdbqt #1/A HIS 61 HE2 -0.031 2.091
2684 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.034 3.344
2685 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A ALA 55 HB2 -0.081 2.961
2686 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 -0.125 2.885
2687 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 HA -0.126 2.886
2688 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A ALA 55 CB -0.136 3.716
2689 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 45 CB -0.155 3.615
2690 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 NE2 -0.167 3.402
2691 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 CA -0.168 3.628
2692 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 CD -0.169 3.749
2693 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 CG -0.185 3.645
2694 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 -0.195 2.955
2695 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 CG -0.207 3.787
2696 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 45 CB -0.220 3.800
2697 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 HA -0.222 2.982
2698 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 HE2 -0.225 3.105
2699 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 55 CB -0.229 3.689
2700 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 HA -0.239 2.999
2701 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 HE2 -0.246 3.126
2702 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.247 3.557
2703 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 HG3 -0.250 3.130
2704 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 CG -0.250 3.560
2705 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 45 HB1 -0.258 3.018
2706 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 CG -0.260 3.720
2707 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 NE2 -0.261 3.766
2708 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A GLU 52 OE1 -0.267 3.507
2709 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A THR 46 O -0.276 3.516
2710 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.276 3.736
2711 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.281 3.591
2712 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 CB -0.323 3.783
2713 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CD2 -0.340 3.800
2714 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 N -0.347 3.732
2715 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 CB -0.361 3.941
2716 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 HB2 -0.382 3.142
2717 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KCX.pdbqt #1/A HIS 61 NE2 -0.387 3.072
2718 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 55 HB3 -0.388 3.148
2719
2720
2721
272241 contacts
2723
2724> hbonds :UNL showDist true radius 0.05 log true saveFile
2725> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
2726> WRM-16.hbonds.txt
2727
2728
2729 Finding intermodel H-bonds
2730 Finding intramodel H-bonds
2731 Constraints relaxed by 0.4 angstroms and 20 degrees
2732 Models used:
2733 1 2KCX.pdbqt
2734 2.1 2KCX--WRM-16.result.pdbqt
2735
2736 1 H-bonds
2737 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2738 2KCX.pdbqt #1/A HIS 61 NE2 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KCX.pdbqt #1/A HIS 61 HE2 3.072 2.091
2739
2740
2741
27421 hydrogen bonds found
2743
2744> select :UNL
2745
274628 atoms, 31 bonds, 1 residue, 1 model selected
2747
2748> label sel text "Ligand "
2749
2750> label height 1
2751
2752> ~select
2753
2754Nothing selected
2755
2756> 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03
2757> ypos .95
2758
2759> 2dlabels text "2KCX WRM-16 Complex" color gray size 18 xpos .03 ypos .91
2760
2761> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
2762> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
2763> true
2764
2765> select :UNL
2766
276728 atoms, 31 bonds, 1 residue, 1 model selected
2768
2769> view sel
2770
2771> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
2772> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
2773> true
2774
2775> close
2776
2777> wait 5
2778
2779> set bgColor white
2780
2781> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1VR2.pdbqt
2782
2783Chain information for 1VR2.pdbqt #1
2784---
2785Chain | Description
2786A | No description available
2787
2788Opened 1VR2.pdbqt containing 1 structures (4310 atoms, 4361 bonds)
2789
2790> wait 5
2791
2792> hide surfaces
2793
2794> hide atoms
2795
2796> show cartoons
2797
2798> wait 5
2799
2800> addh
2801
2802Summary of feedback from adding hydrogens to 1VR2.pdbqt #1
2803---
2804warnings | Not adding hydrogens to /A LYS 838 CB because it is missing heavy-
2805atom bond partners
2806Not adding hydrogens to /A ARG 842 CB because it is missing heavy-atom bond
2807partners
2808Not adding hydrogens to /A PHE 845 CB because it is missing heavy-atom bond
2809partners
2810Not adding hydrogens to /A TYR 938 CB because it is missing heavy-atom bond
2811partners
2812Not adding hydrogens to /A LYS 939 CB because it is missing heavy-atom bond
2813partners
28146 messages similar to the above omitted
2815notes | No usable SEQRES records for 1VR2.pdbqt (#1) chain A; guessing termini
2816instead
2817Chain-initial residues that are actual N termini: /A LEU 820
2818Chain-initial residues that are not actual N termini: /A ASP 998, /A ASP 1064
2819Chain-final residues that are actual C termini: /A ALA 1168
2820Chain-final residues that are not actual C termini: /A LYS 939, /A PHE 1047
2821222 hydrogen bonds
2822Adding 'H' to /A ASP 998
2823Adding 'H' to /A ASP 1064
2824/A LYS 939 is not terminus, removing H atom from 'C'
2825/A PHE 1047 is not terminus, removing H atom from 'C'
28262 hydrogens added
2827
2828
2829> wait 5
2830
2831> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1VR2--
2832> WRM-16.result.pdbqt
2833
2834Summary of feedback from opening
2835/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1VR2--WRM-16.result.pdbqt
2836---
2837warnings | Ignored bad PDB record found on line 2
2838REMARK VINA RESULT: -7.7 0.000 0.000
2839
2840Ignored bad PDB record found on line 3
2841REMARK 5 active torsions:
2842
2843Ignored bad PDB record found on line 4
2844REMARK status: ('A' for Active; 'I' for Inactive)
2845
2846Ignored bad PDB record found on line 5
2847REMARK 1 A between atoms: C_9 and O_15
2848
2849Ignored bad PDB record found on line 6
2850REMARK 2 A between atoms: C_10 and O_17
2851
2852184 messages similar to the above omitted
2853
2854Opened 1VR2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
2855bonds)
2856
2857> wait 5
2858
2859> close #2.2-9
2860
2861> wait 5
2862
2863> contacts :UNL radius 0.05 log true saveFile
2864> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
2865> WRM-16.contacts.txt
2866
2867
2868 Allowed overlap: -0.4
2869 H-bond overlap reduction: 0.4
2870 Ignore contacts between atoms separated by 4 bonds or less
2871 Detect intra-residue contacts: False
2872 Detect intra-molecule contacts: True
2873
2874 47 contacts
2875 atom1 atom2 overlap distance
2876 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLY 846 HA1 0.221 2.659
2877 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A LYS 868 HB1 0.195 2.685
2878 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 HN 0.178 2.582
2879 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 3HG2 0.116 2.764
2880 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 HN 0.070 2.690
2881 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLN 847 HN 0.070 2.810
2882 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 0.032 3.548
2883 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A VAL 848 3HG2 0.032 2.428
2884 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 HB3 -0.025 2.785
2885 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A LYS 868 CB -0.077 3.657
2886 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 CB -0.081 3.541
2887 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLY 846 CA -0.093 3.673
2888 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 2HD1 -0.095 2.855
2889 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 CB -0.107 3.567
2890 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLN 847 N -0.119 3.624
2891 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 HE1 -0.150 2.910
2892 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A PHE 918 CD1 -0.161 3.621
2893 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A PHE 918 HA -0.164 2.924
2894 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 N -0.209 3.594
2895 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A GLN 847 N -0.223 3.608
2896 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 HG2 -0.224 2.984
2897 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 N -0.239 3.624
2898 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A LEU 840 O -0.244 3.184
2899 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A VAL 848 2HG1 -0.254 2.714
2900 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 O -0.260 3.500
2901 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.269 3.729
2902 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.280 3.740
2903 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 3HG2 -0.284 2.894
2904 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 CE -0.291 3.751
2905 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 2HG1 -0.295 2.905
2906 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 CG -0.303 3.763
2907 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 2HD1 -0.308 3.068
2908 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 2HD1 -0.310 3.070
2909 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A VAL 848 CG2 -0.320 3.480
2910 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 HB2 -0.324 2.934
2911 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A PHE 918 CE1 -0.326 3.786
2912 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 HE1 -0.332 3.092
2913 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.343 3.803
2914 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.351 3.811
2915 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 3HG2 -0.354 2.964
2916 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 1HG2 -0.357 3.117
2917 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 1HG2 -0.371 3.131
2918 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 HB1 -0.375 3.135
2919 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 2HG2 -0.383 3.143
2920 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 HB2 -0.387 2.997
2921 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 CD -0.393 3.853
2922 1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 HB2 -0.399 3.159
2923
2924
2925
292647 contacts
2927
2928> hbonds :UNL showDist true radius 0.05 log true saveFile
2929> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
2930> WRM-16.hbonds.txt
2931
2932
2933 Finding intermodel H-bonds
2934 Finding intramodel H-bonds
2935 Constraints relaxed by 0.4 angstroms and 20 degrees
2936 Models used:
2937 1 1VR2.pdbqt
2938 2.1 1VR2--WRM-16.result.pdbqt
2939
2940 0 H-bonds
2941 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2942
2943
2944
29450 hydrogen bonds found
2946
2947> select :UNL
2948
294928 atoms, 31 bonds, 1 residue, 1 model selected
2950
2951> label sel text "Ligand "
2952
2953> label height 1
2954
2955> ~select
2956
2957Nothing selected
2958
2959> 2dlabels text "Binding Energy: -7.7 kcal/mol" color red size 18 xpos .03
2960> ypos .95
2961
2962> 2dlabels text "1VR2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
2963
2964> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
2965> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
2966> true
2967
2968> select :UNL
2969
297028 atoms, 31 bonds, 1 residue, 1 model selected
2971
2972> view sel
2973
2974> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
2975> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
2976> true
2977
2978> close
2979
2980> wait 5
2981
2982> set bgColor white
2983
2984> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5AX3.pdbqt
2985
2986Chain information for 5AX3.pdbqt #1
2987---
2988Chain | Description
2989A | No description available
2990B | No description available
2991
2992Opened 5AX3.pdbqt containing 1 structures (5669 atoms, 5733 bonds)
2993
2994> wait 5
2995
2996> hide surfaces
2997
2998> hide atoms
2999
3000> show cartoons
3001
3002> wait 5
3003
3004> addh
3005
3006Summary of feedback from adding hydrogens to 5AX3.pdbqt #1
3007---
3008notes | No usable SEQRES records for 5AX3.pdbqt (#1) chain A; guessing termini
3009instead
3010No usable SEQRES records for 5AX3.pdbqt (#1) chain B; guessing termini instead
3011Chain-initial residues that are actual N termini: /A GLY 1, /B LEU 349
3012Chain-initial residues that are not actual N termini: /A TYR 27, /A PHE 174,
3013/A THR 181, /A GLY 194, /A LEU 248
3014Chain-final residues that are actual C termini: /A TYR 348, /B GLU 360
3015Chain-final residues that are not actual C termini: /A GLU 24, /A ALA 165, /A
3016VAL 179, /A LEU 191, /A ASP 241
3017195 hydrogen bonds
3018Adding 'H' to /A TYR 27
3019Adding 'H' to /A PHE 174
3020Adding 'H' to /A THR 181
3021Adding 'H' to /A GLY 194
3022Adding 'H' to /A LEU 248
3023/A GLU 24 is not terminus, removing H atom from 'C'
3024/A ALA 165 is not terminus, removing H atom from 'C'
3025/A VAL 179 is not terminus, removing H atom from 'C'
3026/A LEU 191 is not terminus, removing H atom from 'C'
3027/A ASP 241 is not terminus, removing H atom from 'C'
3028-9 hydrogens added
3029
3030
3031> wait 5
3032
3033> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5AX3--
3034> WRM-16.result.pdbqt
3035
3036Summary of feedback from opening
3037/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5AX3--WRM-16.result.pdbqt
3038---
3039warnings | Ignored bad PDB record found on line 2
3040REMARK VINA RESULT: -7.2 0.000 0.000
3041
3042Ignored bad PDB record found on line 3
3043REMARK 5 active torsions:
3044
3045Ignored bad PDB record found on line 4
3046REMARK status: ('A' for Active; 'I' for Inactive)
3047
3048Ignored bad PDB record found on line 5
3049REMARK 1 A between atoms: C_9 and O_15
3050
3051Ignored bad PDB record found on line 6
3052REMARK 2 A between atoms: C_10 and O_17
3053
3054184 messages similar to the above omitted
3055
3056Opened 5AX3--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
3057bonds)
3058
3059> wait 5
3060
3061> close #2.2-9
3062
3063> wait 5
3064
3065> contacts :UNL radius 0.05 log true saveFile
3066> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
3067> WRM-16.contacts.txt
3068
3069
3070 Allowed overlap: -0.4
3071 H-bond overlap reduction: 0.4
3072 Ignore contacts between atoms separated by 4 bonds or less
3073 Detect intra-residue contacts: False
3074 Detect intra-molecule contacts: True
3075
3076 52 contacts
3077 atom1 atom2 overlap distance
3078 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLN 345 HG1 0.154 2.606
3079 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 0.099 2.661
3080 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 HD1 0.056 2.404
3081 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ILE 81 CG2 0.037 3.543
3082 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ILE 81 3HG2 0.002 2.878
3083 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 HD1 -0.003 2.423
3084 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 HG2 -0.004 2.764
3085 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A GLY 13 HA1 -0.068 2.488
3086 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 -0.084 2.844
3087 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HB2 -0.109 2.719
3088 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 13 HA1 -0.127 3.007
3089 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 CD -0.127 3.247
3090 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 15 HE -0.129 2.889
3091 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 82 O -0.141 3.501
3092 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HD2 -0.141 2.901
3093 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ILE 81 2HG2 -0.151 3.031
3094 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLN 345 HG1 -0.154 2.914
3095 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 -0.158 2.768
3096 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.158 2.768
3097 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 CB -0.174 3.294
3098 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 CG -0.181 3.641
3099 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HB2 -0.184 2.794
3100 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ASP 79 OD2 -0.194 3.434
3101 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HB2 -0.210 2.970
3102 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CB -0.218 3.528
3103 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.235 2.845
3104 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 13 HA1 -0.241 3.121
3105 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.249 2.859
3106 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLN 345 CG -0.250 3.710
3107 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 82 O -0.279 3.519
3108 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A GLY 13 CA -0.284 3.404
3109 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 347 HN -0.284 3.044
3110 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 -0.287 3.047
3111 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ILE 81 CG2 -0.288 3.448
3112 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 HB1 -0.297 2.717
3113 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 CD -0.304 3.464
3114 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.311 3.771
3115 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 15 HE -0.322 2.932
3116 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CB -0.324 3.634
3117 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 HN -0.330 2.350
3118 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.346 3.806
3119 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 347 HN -0.347 3.107
3120 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.353 3.663
3121 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 347 N -0.365 3.750
3122 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 HG2 -0.368 3.128
3123 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 346 HB2 -0.371 2.831
3124 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.379 2.989
3125 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.386 2.996
3126 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.388 3.698
3127 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.391 3.851
3128 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HD2 -0.396 3.006
3129 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 HA -0.399 3.159
3130
3131
3132
313352 contacts
3134
3135> hbonds :UNL showDist true radius 0.05 log true saveFile
3136> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
3137> WRM-16.hbonds.txt
3138
3139
3140 Finding intermodel H-bonds
3141 Finding intramodel H-bonds
3142 Constraints relaxed by 0.4 angstroms and 20 degrees
3143 Models used:
3144 1 5AX3.pdbqt
3145 2.1 5AX3--WRM-16.result.pdbqt
3146
3147 1 H-bonds
3148 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
3149 5AX3.pdbqt #1/A ARG 15 N 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 HN 3.304 2.350
3150
3151
3152
31531 hydrogen bonds found
3154
3155> select :UNL
3156
315728 atoms, 31 bonds, 1 residue, 1 model selected
3158
3159> label sel text "Ligand "
3160
3161> label height 1
3162
3163> ~select
3164
3165Nothing selected
3166
3167> 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03
3168> ypos .95
3169
3170> 2dlabels text "5AX3 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
3171
3172> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
3173> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
3174> true
3175
3176> select :UNL
3177
317828 atoms, 31 bonds, 1 residue, 1 model selected
3179
3180> view sel
3181
3182> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
3183> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
3184> true
3185
3186> close
3187
3188> wait 5
3189
3190> set bgColor white
3191
3192> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KMU.pdbqt
3193
3194Chain information for 2KMU.pdbqt #1
3195---
3196Chain | Description
3197A | No description available
3198
3199Opened 2KMU.pdbqt containing 1 structures (957 atoms, 963 bonds)
3200
3201> wait 5
3202
3203> hide surfaces
3204
3205> hide atoms
3206
3207> show cartoons
3208
3209> wait 5
3210
3211> addh
3212
3213Summary of feedback from adding hydrogens to 2KMU.pdbqt #1
3214---
3215notes | No usable SEQRES records for 2KMU.pdbqt (#1) chain A; guessing termini
3216instead
3217Chain-initial residues that are actual N termini: /A GLY 1
3218Chain-initial residues that are not actual N termini:
3219Chain-final residues that are actual C termini: /A GLN 56
3220Chain-final residues that are not actual C termini:
322140 hydrogen bonds
32221 hydrogens added
3223
3224
3225> wait 5
3226
3227> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KMU--
3228> WRM-16.result.pdbqt
3229
3230Summary of feedback from opening
3231/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KMU--WRM-16.result.pdbqt
3232---
3233warnings | Ignored bad PDB record found on line 2
3234REMARK VINA RESULT: -6.8 0.000 0.000
3235
3236Ignored bad PDB record found on line 3
3237REMARK 5 active torsions:
3238
3239Ignored bad PDB record found on line 4
3240REMARK status: ('A' for Active; 'I' for Inactive)
3241
3242Ignored bad PDB record found on line 5
3243REMARK 1 A between atoms: C_9 and O_15
3244
3245Ignored bad PDB record found on line 6
3246REMARK 2 A between atoms: C_10 and O_17
3247
3248184 messages similar to the above omitted
3249
3250Opened 2KMU--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
3251bonds)
3252
3253> wait 5
3254
3255> close #2.2-9
3256
3257> wait 5
3258
3259> contacts :UNL radius 0.05 log true saveFile
3260> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
3261> WRM-16.contacts.txt
3262
3263
3264 Allowed overlap: -0.4
3265 H-bond overlap reduction: 0.4
3266 Ignore contacts between atoms separated by 4 bonds or less
3267 Detect intra-residue contacts: False
3268 Detect intra-molecule contacts: True
3269
3270 55 contacts
3271 atom1 atom2 overlap distance
3272 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 HB2 0.691 2.069
3273 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 CB 0.326 3.134
3274 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 1HH2 0.311 2.449
3275 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 NH2 0.233 3.152
3276 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 HB2 0.185 2.575
3277 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 HE2 0.153 2.727
3278 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 1HH2 0.129 2.631
3279 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HE3 0.035 2.575
3280 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 0.021 2.589
3281 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 OH -0.037 3.147
3282 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A TRP 16 HA -0.042 2.502
3283 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 HD3 -0.069 2.829
3284 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 HH -0.072 2.682
3285 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 CE2 -0.105 3.685
3286 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 HD3 -0.109 2.869
3287 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A ARG 12 NH1 -0.111 2.796
3288 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 CB -0.121 3.581
3289 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 NE -0.127 3.512
3290 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 36 HB1 -0.128 2.738
3291 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 12 NH1 -0.135 3.370
3292 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 HE -0.136 2.896
3293 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A THR 40 2HG2 -0.154 2.914
3294 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.168 3.628
3295 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 NH2 -0.173 3.558
3296 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 -0.176 2.786
3297 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.188 3.648
3298 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HE3 -0.191 2.801
3299 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 12 NH1 -0.202 3.587
3300 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 CE3 -0.202 3.512
3301 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 CB -0.205 3.785
3302 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 CZ -0.217 3.677
3303 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 C -0.231 3.691
3304 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 15 O -0.232 3.592
3305 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 36 HB1 -0.241 3.121
3306 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 CZ3 -0.251 3.561
3307 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 HB1 -0.264 3.144
3308 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.289 3.749
3309 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 -0.305 3.065
3310 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A THR 40 OG1 -0.306 3.566
3311 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.310 3.770
3312 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A TRP 16 CA -0.310 3.470
3313 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 HD2 -0.313 3.073
3314 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PHE 20 N -0.315 3.700
3315 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CG -0.334 3.794
3316 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KMU.pdbqt #1/A PRO 37 HG3 -0.336 3.216
3317 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A ALA 15 O -0.344 3.284
3318 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A ARG 12 2HH1 -0.344 2.404
3319 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 C -0.359 3.819
3320 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PHE 20 N -0.363 3.748
3321 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.364 3.674
3322 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 CZ3 -0.366 3.676
3323 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 36 CB -0.371 3.681
3324 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 OH -0.376 3.756
3325 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 12 1HH1 -0.384 3.144
3326 2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 -0.391 3.001
3327
3328
3329
333055 contacts
3331
3332> hbonds :UNL showDist true radius 0.05 log true saveFile
3333> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
3334> WRM-16.hbonds.txt
3335
3336
3337 Finding intermodel H-bonds
3338 Finding intramodel H-bonds
3339 Constraints relaxed by 0.4 angstroms and 20 degrees
3340 Models used:
3341 1 2KMU.pdbqt
3342 2.1 2KMU--WRM-16.result.pdbqt
3343
3344 0 H-bonds
3345 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
3346
3347
3348
33490 hydrogen bonds found
3350
3351> select :UNL
3352
335328 atoms, 31 bonds, 1 residue, 1 model selected
3354
3355> label sel text "Ligand "
3356
3357> label height 1
3358
3359> ~select
3360
3361Nothing selected
3362
3363> 2dlabels text "Binding Energy: -6.8 kcal/mol" color red size 18 xpos .03
3364> ypos .95
3365
3366> 2dlabels text "2KMU WRM-16 Complex" color gray size 18 xpos .03 ypos .91
3367
3368> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
3369> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
3370> true
3371
3372> select :UNL
3373
337428 atoms, 31 bonds, 1 residue, 1 model selected
3375
3376> view sel
3377
3378> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
3379> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
3380> true
3381
3382> close
3383
3384> wait 5
3385
3386> set bgColor white
3387
3388> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2D68.pdbqt
3389
3390Chain information for 2D68.pdbqt #1
3391---
3392Chain | Description
3393A | No description available
3394B | No description available
3395
3396Opened 2D68.pdbqt containing 1 structures (2419 atoms, 2436 bonds)
3397
3398> wait 5
3399
3400> hide surfaces
3401
3402> hide atoms
3403
3404> show cartoons
3405
3406> wait 5
3407
3408> addh
3409
3410Summary of feedback from adding hydrogens to 2D68.pdbqt #1
3411---
3412warnings | Not adding hydrogens to /A LYS 69 CD because it is missing heavy-
3413atom bond partners
3414Not adding hydrogens to /B LYS 69 CG because it is missing heavy-atom bond
3415partners
3416notes | No usable SEQRES records for 2D68.pdbqt (#1) chain A; guessing termini
3417instead
3418No usable SEQRES records for 2D68.pdbqt (#1) chain B; guessing termini instead
3419Chain-initial residues that are actual N termini: /A VAL 58, /B ASN 59
3420Chain-initial residues that are not actual N termini: /A LEU 104
3421Chain-final residues that are actual C termini: /A TRP 135, /B TRP 135
3422Chain-final residues that are not actual C termini: /A THR 100
3423143 hydrogen bonds
3424Adding 'H' to /A LEU 104
3425/A THR 100 is not terminus, removing H atom from 'C'
3426-3 hydrogens added
3427
3428
3429> wait 5
3430
3431> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D68--
3432> WRM-16.result.pdbqt
3433
3434Summary of feedback from opening
3435/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D68--WRM-16.result.pdbqt
3436---
3437warnings | Ignored bad PDB record found on line 2
3438REMARK VINA RESULT: -6.5 0.000 0.000
3439
3440Ignored bad PDB record found on line 3
3441REMARK 5 active torsions:
3442
3443Ignored bad PDB record found on line 4
3444REMARK status: ('A' for Active; 'I' for Inactive)
3445
3446Ignored bad PDB record found on line 5
3447REMARK 1 A between atoms: C_9 and O_15
3448
3449Ignored bad PDB record found on line 6
3450REMARK 2 A between atoms: C_10 and O_17
3451
3452184 messages similar to the above omitted
3453
3454Opened 2D68--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
3455bonds)
3456
3457> wait 5
3458
3459> close #2.2-9
3460
3461> wait 5
3462
3463> contacts :UNL radius 0.05 log true saveFile
3464> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
3465> WRM-16.contacts.txt
3466
3467
3468 Allowed overlap: -0.4
3469 H-bond overlap reduction: 0.4
3470 Ignore contacts between atoms separated by 4 bonds or less
3471 Detect intra-residue contacts: False
3472 Detect intra-molecule contacts: True
3473
3474 45 contacts
3475 atom1 atom2 overlap distance
3476 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD2 0.473 2.407
3477 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD1 0.376 2.384
3478 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 HB1 0.240 2.640
3479 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 HA 0.211 2.669
3480 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CD 0.179 3.281
3481 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B PHE 65 HD1 0.147 2.733
3482 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CD 0.095 3.485
3483 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD1 0.057 2.703
3484 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 HD1 0.023 2.437
3485 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 HA 0.004 2.456
3486 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CB -0.002 3.582
3487 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 HD1 -0.029 2.449
3488 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CD1 -0.031 3.151
3489 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A PHE 85 HZ -0.041 2.461
3490 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.069 2.829
3491 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 CZ -0.108 3.568
3492 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A GLY 124 O -0.108 3.468
3493 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D68.pdbqt #1/A PHE 84 O -0.119 3.479
3494 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CA -0.139 3.719
3495 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.157 2.917
3496 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 O -0.164 3.404
3497 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CA -0.169 3.329
3498 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A PHE 85 CZ -0.174 3.294
3499 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B PHE 65 CD1 -0.195 3.775
3500 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A PHE 84 HE2 -0.224 2.684
3501 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 CE2 -0.261 3.721
3502 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CD1 -0.269 3.429
3503 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 CZ -0.272 3.582
3504 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CD -0.275 3.735
3505 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.282 2.892
3506 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.283 3.043
3507 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.310 3.070
3508 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D68.pdbqt #1/A PHE 84 CE1 -0.322 3.902
3509 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A GLY 124 O -0.324 3.414
3510 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD2 -0.344 3.104
3511 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B SER 61 HB1 -0.355 2.815
3512 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A GLY 124 O -0.356 3.296
3513 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CB -0.368 3.828
3514 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D68.pdbqt #1/A PHE 84 CD1 -0.372 3.952
3515 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CB -0.384 3.844
3516 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.385 2.995
3517 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CA -0.390 3.970
3518 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 HB1 -0.391 3.151
3519 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CB -0.395 3.705
3520 2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CB -0.395 3.555
3521
3522
3523
352445 contacts
3525
3526> hbonds :UNL showDist true radius 0.05 log true saveFile
3527> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
3528> WRM-16.hbonds.txt
3529
3530
3531 Finding intermodel H-bonds
3532 Finding intramodel H-bonds
3533 Constraints relaxed by 0.4 angstroms and 20 degrees
3534 Models used:
3535 1 2D68.pdbqt
3536 2.1 2D68--WRM-16.result.pdbqt
3537
3538 0 H-bonds
3539 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
3540
3541
3542
35430 hydrogen bonds found
3544
3545> select :UNL
3546
354728 atoms, 31 bonds, 1 residue, 1 model selected
3548
3549> label sel text "Ligand "
3550
3551> label height 1
3552
3553> ~select
3554
3555Nothing selected
3556
3557> 2dlabels text "Binding Energy: -6.5 kcal/mol" color red size 18 xpos .03
3558> ypos .95
3559
3560> 2dlabels text "2D68 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
3561
3562> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
3563> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
3564> true
3565
3566> select :UNL
3567
356828 atoms, 31 bonds, 1 residue, 1 model selected
3569
3570> view sel
3571
3572> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
3573> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
3574> true
3575
3576> close
3577
3578> wait 5
3579
3580> set bgColor white
3581
3582> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1OW1.pdbqt
3583
3584Chain information for 1OW1.pdbqt #1
3585---
3586Chain | Description
3587A | No description available
3588
3589Opened 1OW1.pdbqt containing 1 structures (2619 atoms, 2644 bonds)
3590
3591> wait 5
3592
3593> hide surfaces
3594
3595> hide atoms
3596
3597> show cartoons
3598
3599> wait 5
3600
3601> addh
3602
3603Summary of feedback from adding hydrogens to 1OW1.pdbqt #1
3604---
3605notes | No usable SEQRES records for 1OW1.pdbqt (#1) chain A; guessing termini
3606instead
3607Chain-initial residues that are actual N termini: /A PRO 3495
3608Chain-initial residues that are not actual N termini: /A PRO 3545
3609Chain-final residues that are actual C termini: /A VAL 3664
3610Chain-final residues that are not actual C termini: /A SER 3541
3611124 hydrogen bonds
3612/A SER 3541 is not terminus, removing H atom from 'C'
36130 hydrogens added
3614
3615
3616> wait 5
3617
3618> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OW1--
3619> WRM-16.result.pdbqt
3620
3621Summary of feedback from opening
3622/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OW1--WRM-16.result.pdbqt
3623---
3624warnings | Ignored bad PDB record found on line 2
3625REMARK VINA RESULT: -7.1 0.000 0.000
3626
3627Ignored bad PDB record found on line 3
3628REMARK 5 active torsions:
3629
3630Ignored bad PDB record found on line 4
3631REMARK status: ('A' for Active; 'I' for Inactive)
3632
3633Ignored bad PDB record found on line 5
3634REMARK 1 A between atoms: C_9 and O_15
3635
3636Ignored bad PDB record found on line 6
3637REMARK 2 A between atoms: C_10 and O_17
3638
3639184 messages similar to the above omitted
3640
3641Opened 1OW1--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
3642bonds)
3643
3644> wait 5
3645
3646> close #2.2-9
3647
3648> wait 5
3649
3650> contacts :UNL radius 0.05 log true saveFile
3651> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
3652> WRM-16.contacts.txt
3653
3654
3655 Allowed overlap: -0.4
3656 H-bond overlap reduction: 0.4
3657 Ignore contacts between atoms separated by 4 bonds or less
3658 Detect intra-residue contacts: False
3659 Detect intra-molecule contacts: True
3660
3661 54 contacts
3662 atom1 atom2 overlap distance
3663 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB2 0.457 2.423
3664 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A HIS 3656 HE1 0.285 2.595
3665 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 1HG2 0.241 2.639
3666 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 HD2 0.208 2.552
3667 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A HIS 3656 CE1 0.058 3.522
3668 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 ND2 0.047 3.188
3669 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB 0.042 3.538
3670 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 1HD2 0.027 2.583
3671 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 1HE2 0.008 2.602
3672 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A GLN 3604 1HE2 0.006 2.054
3673 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLU 3636 OE2 -0.046 3.286
3674 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 CG2 -0.051 3.511
3675 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HG2 -0.056 2.936
3676 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 CD -0.060 3.520
3677 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB2 -0.069 2.679
3678 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A PRO 3655 HG1 -0.070 2.490
3679 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 2HD1 -0.102 2.982
3680 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 ND2 -0.113 2.798
3681 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A LYS 3596 HG1 -0.117 2.537
3682 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 CG2 -0.123 3.703
3683 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OW1.pdbqt #1/A THR 3601 OG1 -0.128 3.508
3684 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 1HD2 -0.143 2.203
3685 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 OE1 -0.160 3.400
3686 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB -0.161 3.471
3687 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLU 3636 CD -0.162 3.622
3688 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB1 -0.171 2.781
3689 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 1HG2 -0.189 2.799
3690 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A PRO 3655 CG -0.210 3.330
3691 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 1HG2 -0.214 2.974
3692 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A SER 3651 HA -0.252 3.132
3693 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB1 -0.262 2.872
3694 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 HN -0.264 2.284
3695 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB -0.265 3.575
3696 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB -0.274 3.584
3697 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A LYS 3596 CG -0.287 3.407
3698 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 OE1 -0.287 3.527
3699 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A PRO 3655 CB -0.295 3.415
3700 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 HN -0.297 2.357
3701 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CG -0.300 3.880
3702 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB1 -0.312 2.922
3703 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLU 3636 CD -0.313 3.773
3704 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 CG -0.322 3.782
3705 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 HB1 -0.332 3.092
3706 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 N -0.332 2.977
3707 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 NE2 -0.343 3.578
3708 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 3HG2 -0.343 3.103
3709 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 CA -0.344 3.464
3710 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 HN -0.347 3.227
3711 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A GLN 3604 NE2 -0.358 3.043
3712 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A LYS 3596 CD -0.367 3.487
3713 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 NE2 -0.367 3.752
3714 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 1HD2 -0.377 2.987
3715 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB2 -0.377 2.987
3716 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 HN -0.390 3.000
3717
3718
3719
372054 contacts
3721
3722> hbonds :UNL showDist true radius 0.05 log true saveFile
3723> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
3724> WRM-16.hbonds.txt
3725
3726
3727 Finding intermodel H-bonds
3728 Finding intramodel H-bonds
3729 Constraints relaxed by 0.4 angstroms and 20 degrees
3730 Models used:
3731 1 1OW1.pdbqt
3732 2.1 1OW1--WRM-16.result.pdbqt
3733
3734 2 H-bonds
3735 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
3736 1OW1.pdbqt #1/A GLN 3604 NE2 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A GLN 3604 1HE2 3.043 2.054
3737 1OW1.pdbqt #1/A ASN 3652 N 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 HN 3.284 2.357
3738
3739
3740
37412 hydrogen bonds found
3742
3743> select :UNL
3744
374528 atoms, 31 bonds, 1 residue, 1 model selected
3746
3747> label sel text "Ligand "
3748
3749> label height 1
3750
3751> ~select
3752
3753Nothing selected
3754
3755> 2dlabels text "Binding Energy: -7.1 kcal/mol" color red size 18 xpos .03
3756> ypos .95
3757
3758> 2dlabels text "1OW1 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
3759
3760> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
3761> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
3762> true
3763
3764> select :UNL
3765
376628 atoms, 31 bonds, 1 residue, 1 model selected
3767
3768> view sel
3769
3770> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
3771> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
3772> true
3773
3774> close
3775
3776> wait 5
3777
3778> set bgColor white
3779
3780> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1RJB.pdbqt
3781
3782Chain information for 1RJB.pdbqt #1
3783---
3784Chain | Description
3785A | No description available
3786
3787Opened 1RJB.pdbqt containing 1 structures (4781 atoms, 4839 bonds)
3788
3789> wait 5
3790
3791> hide surfaces
3792
3793> hide atoms
3794
3795> show cartoons
3796
3797> wait 5
3798
3799> addh
3800
3801Summary of feedback from adding hydrogens to 1RJB.pdbqt #1
3802---
3803notes | No usable SEQRES records for 1RJB.pdbqt (#1) chain A; guessing termini
3804instead
3805Chain-initial residues that are actual N termini: /A TYR 572
3806Chain-initial residues that are not actual N termini: /A ARG 655, /A LEU 783
3807Chain-final residues that are actual C termini: /A LEU 947
3808Chain-final residues that are not actual C termini: /A GLU 648, /A PHE 710
3809249 hydrogen bonds
3810Adding 'H' to /A ARG 655
3811Adding 'H' to /A LEU 783
3812/A GLU 648 is not terminus, removing H atom from 'C'
3813/A PHE 710 is not terminus, removing H atom from 'C'
38143 hydrogens added
3815
3816
3817> wait 5
3818
3819> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RJB--
3820> WRM-16.result.pdbqt
3821
3822Summary of feedback from opening
3823/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RJB--WRM-16.result.pdbqt
3824---
3825warnings | Ignored bad PDB record found on line 2
3826REMARK VINA RESULT: -8.6 0.000 0.000
3827
3828Ignored bad PDB record found on line 3
3829REMARK 5 active torsions:
3830
3831Ignored bad PDB record found on line 4
3832REMARK status: ('A' for Active; 'I' for Inactive)
3833
3834Ignored bad PDB record found on line 5
3835REMARK 1 A between atoms: C_9 and O_15
3836
3837Ignored bad PDB record found on line 6
3838REMARK 2 A between atoms: C_10 and O_17
3839
3840184 messages similar to the above omitted
3841
3842Opened 1RJB--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
3843bonds)
3844
3845> wait 5
3846
3847> close #2.2-9
3848
3849> wait 5
3850
3851> contacts :UNL radius 0.05 log true saveFile
3852> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
3853> WRM-16.contacts.txt
3854
3855
3856 Allowed overlap: -0.4
3857 H-bond overlap reduction: 0.4
3858 Ignore contacts between atoms separated by 4 bonds or less
3859 Detect intra-residue contacts: False
3860 Detect intra-molecule contacts: True
3861
3862 51 contacts
3863 atom1 atom2 overlap distance
3864 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 2HE2 0.378 2.502
3865 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 2HG2 0.292 2.468
3866 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 NE2 0.238 3.267
3867 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A PHE 621 HE2 0.094 2.666
3868 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A TYR 865 HH 0.037 2.723
3869 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O 0.021 3.069
3870 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 1HG1 -0.003 2.763
3871 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CG -0.016 3.596
3872 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ALA 848 HB3 -0.091 2.851
3873 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HB1 -0.091 2.701
3874 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.093 3.403
3875 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 CG2 -0.117 3.577
3876 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HG1 -0.148 2.908
3877 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ARG 810 HD2 -0.162 2.582
3878 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HN -0.174 2.784
3879 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HG1 -0.178 2.938
3880 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A LEU 850 1HD2 -0.179 2.939
3881 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A TYR 842 CE1 -0.179 3.339
3882 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A LEU 850 1HD2 -0.188 2.948
3883 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A PHE 621 CE2 -0.192 3.652
3884 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 2HG2 -0.200 2.960
3885 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ALA 848 HA -0.214 2.674
3886 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ARG 810 CD -0.219 3.339
3887 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 HG2 -0.221 3.101
3888 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 CG -0.223 3.683
3889 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ASP 811 HB2 -0.228 2.648
3890 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A GLN 575 HG2 -0.230 2.650
3891 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 CG -0.243 3.703
3892 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A LEU 850 CD2 -0.254 3.714
3893 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 HG1 -0.259 3.139
3894 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.259 3.839
3895 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A TYR 865 OH -0.259 3.519
3896 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 OE1 -0.268 3.358
3897 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O -0.269 3.359
3898 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ALA 848 CB -0.277 3.737
3899 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O -0.297 3.387
3900 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O -0.301 3.391
3901 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HG2 -0.313 3.073
3902 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 NE2 -0.318 3.553
3903 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HB1 -0.331 3.091
3904 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 OE1 -0.332 3.692
3905 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 NE2 -0.352 3.857
3906 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.357 3.667
3907 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 OE1 -0.366 3.726
3908 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A TYR 842 HE1 -0.375 2.835
3909 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ARG 810 CZ -0.376 3.496
3910 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ASP 811 OD1 -0.387 3.747
3911 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.389 3.969
3912 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HB1 -0.395 3.005
3913 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 CG1 -0.395 3.855
3914 1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ASP 811 CB -0.397 3.517
3915
3916
3917
391851 contacts
3919
3920> hbonds :UNL showDist true radius 0.05 log true saveFile
3921> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
3922> WRM-16.hbonds.txt
3923
3924
3925 Finding intermodel H-bonds
3926 Finding intramodel H-bonds
3927 Constraints relaxed by 0.4 angstroms and 20 degrees
3928 Models used:
3929 1 1RJB.pdbqt
3930 2.1 1RJB--WRM-16.result.pdbqt
3931
3932 0 H-bonds
3933 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
3934
3935
3936
39370 hydrogen bonds found
3938
3939> select :UNL
3940
394128 atoms, 31 bonds, 1 residue, 1 model selected
3942
3943> label sel text "Ligand "
3944
3945> label height 1
3946
3947> ~select
3948
3949Nothing selected
3950
3951> 2dlabels text "Binding Energy: -8.6 kcal/mol" color red size 18 xpos .03
3952> ypos .95
3953
3954> 2dlabels text "1RJB WRM-16 Complex" color gray size 18 xpos .03 ypos .91
3955
3956> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
3957> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
3958> true
3959
3960> select :UNL
3961
396228 atoms, 31 bonds, 1 residue, 1 model selected
3963
3964> view sel
3965
3966> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
3967> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
3968> true
3969
3970> close
3971
3972> wait 5
3973
3974> set bgColor white
3975
3976> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1IFR.pdbqt
3977
3978Chain information for 1IFR.pdbqt #1
3979---
3980Chain | Description
3981A | No description available
3982
3983Opened 1IFR.pdbqt containing 1 structures (1747 atoms, 1765 bonds)
3984
3985> wait 5
3986
3987> hide surfaces
3988
3989> hide atoms
3990
3991> show cartoons
3992
3993> wait 5
3994
3995> addh
3996
3997Summary of feedback from adding hydrogens to 1IFR.pdbqt #1
3998---
3999notes | No usable SEQRES records for 1IFR.pdbqt (#1) chain A; guessing termini
4000instead
4001Chain-initial residues that are actual N termini: /A GLY 432
4002Chain-initial residues that are not actual N termini:
4003Chain-final residues that are actual C termini: /A VAL 544
4004Chain-final residues that are not actual C termini:
400596 hydrogen bonds
40061 hydrogens added
4007
4008
4009> wait 5
4010
4011> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1IFR--
4012> WRM-16.result.pdbqt
4013
4014Summary of feedback from opening
4015/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1IFR--WRM-16.result.pdbqt
4016---
4017warnings | Ignored bad PDB record found on line 2
4018REMARK VINA RESULT: -6.7 0.000 0.000
4019
4020Ignored bad PDB record found on line 3
4021REMARK 5 active torsions:
4022
4023Ignored bad PDB record found on line 4
4024REMARK status: ('A' for Active; 'I' for Inactive)
4025
4026Ignored bad PDB record found on line 5
4027REMARK 1 A between atoms: C_9 and O_15
4028
4029Ignored bad PDB record found on line 6
4030REMARK 2 A between atoms: C_10 and O_17
4031
4032184 messages similar to the above omitted
4033
4034Opened 1IFR--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
4035bonds)
4036
4037> wait 5
4038
4039> close #2.2-9
4040
4041> wait 5
4042
4043> contacts :UNL radius 0.05 log true saveFile
4044> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
4045> WRM-16.contacts.txt
4046
4047
4048 Allowed overlap: -0.4
4049 H-bond overlap reduction: 0.4
4050 Ignore contacts between atoms separated by 4 bonds or less
4051 Detect intra-residue contacts: False
4052 Detect intra-molecule contacts: True
4053
4054 43 contacts
4055 atom1 atom2 overlap distance
4056 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 HE1 0.513 2.367
4057 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 CE1 0.243 3.337
4058 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A PRO 484 HA 0.157 2.723
4059 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HD2 0.117 2.643
4060 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TRP 514 HE1 0.011 2.869
4061 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.034 3.494
4062 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A TRP 514 HD1 -0.075 2.495
4063 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ALA 516 HB1 -0.130 3.010
4064 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ALA 516 CB -0.132 3.712
4065 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.132 3.442
4066 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CB -0.156 3.616
4067 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A PRO 484 CA -0.164 3.744
4068 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CD -0.170 3.630
4069 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A VAL 513 O -0.173 3.533
4070 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.177 2.937
4071 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A LYS 515 HN -0.199 2.809
4072 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A PRO 484 HG1 -0.203 2.963
4073 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.212 2.972
4074 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A VAL 513 O -0.218 3.458
4075 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TRP 514 NE1 -0.230 3.735
4076 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.238 3.698
4077 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A LYS 515 HB2 -0.256 2.676
4078 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A LEU 512 HB1 -0.279 2.699
4079 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.284 3.044
4080 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 OH -0.290 3.670
4081 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TRP 514 HD1 -0.300 2.910
4082 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A PRO 484 HG1 -0.303 2.723
4083 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CB -0.312 3.772
4084 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 NE2 -0.315 3.700
4085 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A PRO 484 HA -0.316 2.776
4086 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.321 3.781
4087 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A ALA 516 HN -0.348 2.368
4088 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CB -0.362 3.822
4089 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HD2 -0.363 3.123
4090 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.365 3.125
4091 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 ND1 -0.367 3.752
4092 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 CZ -0.368 3.948
4093 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB2 -0.368 3.128
4094 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CD -0.382 3.842
4095 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 HE1 -0.384 2.994
4096 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A HIS 506 HE1 -0.385 2.805
4097 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A TRP 514 CD1 -0.396 3.516
4098 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 O -0.398 3.488
4099
4100
4101
410243 contacts
4103
4104> hbonds :UNL showDist true radius 0.05 log true saveFile
4105> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
4106> WRM-16.hbonds.txt
4107
4108
4109 Finding intermodel H-bonds
4110 Finding intramodel H-bonds
4111 Constraints relaxed by 0.4 angstroms and 20 degrees
4112 Models used:
4113 1 1IFR.pdbqt
4114 2.1 1IFR--WRM-16.result.pdbqt
4115
4116 2 H-bonds
4117 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
4118 1IFR.pdbqt #1/A LYS 515 N 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A LYS 515 HN 3.558 2.542
4119 1IFR.pdbqt #1/A ALA 516 N 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A ALA 516 HN 3.125 2.368
4120
4121
4122
41232 hydrogen bonds found
4124
4125> select :UNL
4126
412728 atoms, 31 bonds, 1 residue, 1 model selected
4128
4129> label sel text "Ligand "
4130
4131> label height 1
4132
4133> ~select
4134
4135Nothing selected
4136
4137> 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
4138> ypos .95
4139
4140> 2dlabels text "1IFR WRM-16 Complex" color gray size 18 xpos .03 ypos .91
4141
4142> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
4143> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
4144> true
4145
4146> select :UNL
4147
414828 atoms, 31 bonds, 1 residue, 1 model selected
4149
4150> view sel
4151
4152> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
4153> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
4154> true
4155
4156> close
4157
4158> wait 5
4159
4160> set bgColor white
4161
4162> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1DNQ.pdbqt
4163
4164Chain information for 1DNQ.pdbqt #1
4165---
4166Chain | Description
4167A | No description available
4168
4169Opened 1DNQ.pdbqt containing 1 structures (4770 atoms, 4812 bonds)
4170
4171> wait 5
4172
4173> hide surfaces
4174
4175> hide atoms
4176
4177> show cartoons
4178
4179> wait 5
4180
4181> addh
4182
4183Summary of feedback from adding hydrogens to 1DNQ.pdbqt #1
4184---
4185notes | No usable SEQRES records for 1DNQ.pdbqt (#1) chain A; guessing termini
4186instead
4187Chain-initial residues that are actual N termini: /A LEU 1
4188Chain-initial residues that are not actual N termini:
4189Chain-final residues that are actual C termini: /A VAL 312
4190Chain-final residues that are not actual C termini:
4191155 hydrogen bonds
419226 hydrogens added
4193
4194
4195> wait 5
4196
4197> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1DNQ--
4198> WRM-16.result.pdbqt
4199
4200Summary of feedback from opening
4201/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1DNQ--WRM-16.result.pdbqt
4202---
4203warnings | Ignored bad PDB record found on line 2
4204REMARK VINA RESULT: -7.9 0.000 0.000
4205
4206Ignored bad PDB record found on line 3
4207REMARK 5 active torsions:
4208
4209Ignored bad PDB record found on line 4
4210REMARK status: ('A' for Active; 'I' for Inactive)
4211
4212Ignored bad PDB record found on line 5
4213REMARK 1 A between atoms: C_9 and O_15
4214
4215Ignored bad PDB record found on line 6
4216REMARK 2 A between atoms: C_10 and O_17
4217
4218184 messages similar to the above omitted
4219
4220Opened 1DNQ--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
4221bonds)
4222
4223> wait 5
4224
4225> close #2.2-9
4226
4227> wait 5
4228
4229> contacts :UNL radius 0.05 log true saveFile
4230> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
4231> WRM-16.contacts.txt
4232
4233
4234 Allowed overlap: -0.4
4235 H-bond overlap reduction: 0.4
4236 Ignore contacts between atoms separated by 4 bonds or less
4237 Detect intra-residue contacts: False
4238 Detect intra-molecule contacts: True
4239
4240 44 contacts
4241 atom1 atom2 overlap distance
4242 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 HN 0.298 2.582
4243 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CD1 0.113 3.467
4244 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 0.112 2.648
4245 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A ASN 70 1HD2 0.109 1.911
4246 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 HG2 0.095 2.665
4247 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 68 HB2 0.074 2.686
4248 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 N 0.071 3.434
4249 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.020 2.780
4250 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 HB1 -0.041 2.921
4251 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HA -0.076 2.836
4252 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.088 2.698
4253 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.089 2.849
4254 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 HD1 -0.098 2.978
4255 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 HA -0.117 2.877
4256 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A TYR 45 HE1 -0.135 2.555
4257 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CE2 -0.142 3.452
4258 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 68 CB -0.172 3.632
4259 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 CG -0.199 3.659
4260 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.208 2.968
4261 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 70 1HD2 -0.212 2.822
4262 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 CB -0.218 3.798
4263 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 104 C -0.227 3.687
4264 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 CA -0.229 3.689
4265 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CA -0.237 3.697
4266 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 N -0.252 3.637
4267 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.253 3.713
4268 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A ALA 68 HB3 -0.257 3.137
4269 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.260 3.720
4270 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A ALA 68 CB -0.260 3.840
4271 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A ASN 70 ND2 -0.271 2.916
4272 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 70 OD1 -0.279 3.519
4273 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 CA -0.290 3.870
4274 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 HA -0.291 3.051
4275 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CD2 -0.304 3.614
4276 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.326 2.936
4277 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CZ -0.334 3.644
4278 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.353 3.663
4279 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HB1 -0.356 2.966
4280 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 70 OD1 -0.365 3.455
4281 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CE2 -0.368 3.678
4282 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.383 3.843
4283 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.385 3.845
4284 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 68 C -0.385 3.845
4285 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 103 O -0.388 3.628
4286
4287
4288
428944 contacts
4290
4291> hbonds :UNL showDist true radius 0.05 log true saveFile
4292> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
4293> WRM-16.hbonds.txt
4294
4295
4296 Finding intermodel H-bonds
4297 Finding intramodel H-bonds
4298 Constraints relaxed by 0.4 angstroms and 20 degrees
4299 Models used:
4300 1 1DNQ.pdbqt
4301 2.1 1DNQ--WRM-16.result.pdbqt
4302
4303 1 H-bonds
4304 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
4305 1DNQ.pdbqt #1/A ASN 70 ND2 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A ASN 70 1HD2 2.916 1.911
4306
4307
4308
43091 hydrogen bonds found
4310
4311> select :UNL
4312
431328 atoms, 31 bonds, 1 residue, 1 model selected
4314
4315> label sel text "Ligand "
4316
4317> label height 1
4318
4319> ~select
4320
4321Nothing selected
4322
4323> 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
4324> ypos .95
4325
4326> 2dlabels text "1DNQ WRM-16 Complex" color gray size 18 xpos .03 ypos .91
4327
4328> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
4329> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
4330> true
4331
4332> select :UNL
4333
433428 atoms, 31 bonds, 1 residue, 1 model selected
4335
4336> view sel
4337
4338> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
4339> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
4340> true
4341
4342> close
4343
4344> wait 5
4345
4346> set bgColor white
4347
4348> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3U84.pdbqt
4349
4350Chain information for 3U84.pdbqt #1
4351---
4352Chain | Description
4353A | No description available
4354B | No description available
4355
4356Opened 3U84.pdbqt containing 1 structures (15424 atoms, 15596 bonds)
4357
4358> wait 5
4359
4360> hide surfaces
4361
4362> hide atoms
4363
4364> show cartoons
4365
4366> wait 5
4367
4368> addh
4369
4370Summary of feedback from adding hydrogens to 3U84.pdbqt #1
4371---
4372warnings | Not adding hydrogens to /B ARG 206 CB because it is missing heavy-
4373atom bond partners
4374Not adding hydrogens to /B ARG 207 CB because it is missing heavy-atom bond
4375partners
4376notes | No usable SEQRES records for 3U84.pdbqt (#1) chain A; guessing termini
4377instead
4378No usable SEQRES records for 3U84.pdbqt (#1) chain B; guessing termini instead
4379Chain-initial residues that are actual N termini: /A SER 1, /B GLY 2
4380Chain-initial residues that are not actual N termini: /A SER 402, /A THR 534,
4381/A GLY 548, /A SER 596, /B LEU 75, /B ARG 206, /B SER 402, /B ALA 523, /B GLY
4382548
4383Chain-final residues that are actual C termini: /A LYS 608, /B ALA 581
4384Chain-final residues that are not actual C termini: /A GLY 386, /A GLY 528, /A
4385ALA 539, /A ALA 581, /B ASP 70, /B HIS 199, /B ALA 385, /B SER 459, /B GLY 528
4386784 hydrogen bonds
4387Adding 'H' to /A SER 402
4388Adding 'H' to /A THR 534
4389Adding 'H' to /A GLY 548
4390Adding 'H' to /A SER 596
4391Adding 'H' to /B LEU 75
43924 messages similar to the above omitted
4393/A GLY 386 is not terminus, removing H atom from 'C'
4394/A GLY 528 is not terminus, removing H atom from 'C'
4395/A ALA 539 is not terminus, removing H atom from 'C'
4396/A ALA 581 is not terminus, removing H atom from 'C'
4397/B ASP 70 is not terminus, removing H atom from 'C'
43984 messages similar to the above omitted
4399-13 hydrogens added
4400
4401
4402> wait 5
4403
4404> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3U84--
4405> WRM-16.result.pdbqt
4406
4407Summary of feedback from opening
4408/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3U84--WRM-16.result.pdbqt
4409---
4410warnings | Ignored bad PDB record found on line 2
4411REMARK VINA RESULT: -7.5 0.000 0.000
4412
4413Ignored bad PDB record found on line 3
4414REMARK 5 active torsions:
4415
4416Ignored bad PDB record found on line 4
4417REMARK status: ('A' for Active; 'I' for Inactive)
4418
4419Ignored bad PDB record found on line 5
4420REMARK 1 A between atoms: C_9 and O_15
4421
4422Ignored bad PDB record found on line 6
4423REMARK 2 A between atoms: C_10 and O_17
4424
4425184 messages similar to the above omitted
4426
4427Opened 3U84--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
4428bonds)
4429
4430> wait 5
4431
4432> close #2.2-9
4433
4434> wait 5
4435
4436> contacts :UNL radius 0.05 log true saveFile
4437> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
4438> WRM-16.contacts.txt
4439
4440
4441 Allowed overlap: -0.4
4442 H-bond overlap reduction: 0.4
4443 Ignore contacts between atoms separated by 4 bonds or less
4444 Detect intra-residue contacts: False
4445 Detect intra-molecule contacts: True
4446
4447 37 contacts
4448 atom1 atom2 overlap distance
4449 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 HB2 0.433 2.027
4450 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TRP 341 HZ2 0.260 2.620
4451 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B VAL 371 1HG1 0.250 2.630
4452 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLY 326 HA1 0.185 2.695
4453 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B CYS 329 HG 0.091 2.789
4454 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 CB 0.060 3.100
4455 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLU 363 OE2 -0.030 3.390
4456 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 319 CD2 -0.086 3.546
4457 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B VAL 371 CG1 -0.103 3.683
4458 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TRP 341 HE1 -0.116 2.136
4459 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TRP 341 CZ2 -0.126 3.706
4460 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 HB1 -0.165 2.585
4461 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLY 326 CA -0.175 3.755
4462 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 HB2 -0.189 3.069
4463 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 O -0.208 3.148
4464 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CE1 -0.214 3.674
4465 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B VAL 371 1HG2 -0.215 2.675
4466 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CE2 -0.234 3.694
4467 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B CYS 329 SG -0.241 3.903
4468 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 CB -0.245 3.365
4469 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 HA -0.261 3.141
4470 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 C -0.269 3.429
4471 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 319 CE2 -0.282 3.742
4472 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CZ -0.292 3.752
4473 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CZ -0.312 3.772
4474 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TYR 323 CD2 -0.317 3.437
4475 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 C -0.325 3.445
4476 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 OH -0.327 3.587
4477 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 OH -0.330 3.440
4478 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 C -0.334 3.914
4479 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 319 CG -0.349 3.809
4480 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 OH -0.353 3.613
4481 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CZ -0.360 3.670
4482 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TYR 323 N -0.378 3.023
4483 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 HB2 -0.382 2.992
4484 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLU 363 OE2 -0.387 3.477
4485 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 O -0.399 3.759
4486
4487
4488
448937 contacts
4490
4491> hbonds :UNL showDist true radius 0.05 log true saveFile
4492> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
4493> WRM-16.hbonds.txt
4494
4495
4496 Finding intermodel H-bonds
4497 Finding intramodel H-bonds
4498 Constraints relaxed by 0.4 angstroms and 20 degrees
4499 Models used:
4500 1 3U84.pdbqt
4501 2.1 3U84--WRM-16.result.pdbqt
4502
4503 1 H-bonds
4504 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
4505 3U84.pdbqt #1/B TRP 341 NE1 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TRP 341 HE1 3.103 2.136
4506
4507
4508
45091 hydrogen bonds found
4510
4511> select :UNL
4512
451328 atoms, 31 bonds, 1 residue, 1 model selected
4514
4515> label sel text "Ligand "
4516
4517> label height 1
4518
4519> ~select
4520
4521Nothing selected
4522
4523> 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03
4524> ypos .95
4525
4526> 2dlabels text "3U84 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
4527
4528> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
4529> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
4530> true
4531
4532> select :UNL
4533
453428 atoms, 31 bonds, 1 residue, 1 model selected
4535
4536> view sel
4537
4538> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
4539> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
4540> true
4541
4542> close
4543
4544> wait 5
4545
4546> set bgColor white
4547
4548> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2YSM.pdbqt
4549
4550Chain information for 2YSM.pdbqt #1
4551---
4552Chain | Description
4553A | No description available
4554
4555Opened 2YSM.pdbqt containing 1 structures (1584 atoms, 1601 bonds)
4556
4557> wait 5
4558
4559> hide surfaces
4560
4561> hide atoms
4562
4563> show cartoons
4564
4565> wait 5
4566
4567> addh
4568
4569Summary of feedback from adding hydrogens to 2YSM.pdbqt #1
4570---
4571notes | No usable SEQRES records for 2YSM.pdbqt (#1) chain A; guessing termini
4572instead
4573Chain-initial residues that are actual N termini: /A GLY 1
4574Chain-initial residues that are not actual N termini:
4575Chain-final residues that are actual C termini: /A GLY 111
4576Chain-final residues that are not actual C termini:
457729 hydrogen bonds
457815 hydrogens added
4579
4580
4581> wait 5
4582
4583> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2YSM--
4584> WRM-16.result.pdbqt
4585
4586Summary of feedback from opening
4587/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2YSM--WRM-16.result.pdbqt
4588---
4589warnings | Ignored bad PDB record found on line 2
4590REMARK VINA RESULT: -7.5 0.000 0.000
4591
4592Ignored bad PDB record found on line 3
4593REMARK 5 active torsions:
4594
4595Ignored bad PDB record found on line 4
4596REMARK status: ('A' for Active; 'I' for Inactive)
4597
4598Ignored bad PDB record found on line 5
4599REMARK 1 A between atoms: C_9 and O_15
4600
4601Ignored bad PDB record found on line 6
4602REMARK 2 A between atoms: C_10 and O_17
4603
4604184 messages similar to the above omitted
4605
4606Opened 2YSM--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
4607bonds)
4608
4609> wait 5
4610
4611> close #2.2-9
4612
4613> wait 5
4614
4615> contacts :UNL radius 0.05 log true saveFile
4616> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
4617> WRM-16.contacts.txt
4618
4619
4620 Allowed overlap: -0.4
4621 H-bond overlap reduction: 0.4
4622 Ignore contacts between atoms separated by 4 bonds or less
4623 Detect intra-residue contacts: False
4624 Detect intra-molecule contacts: True
4625
4626 58 contacts
4627 atom1 atom2 overlap distance
4628 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 HG2 0.549 2.331
4629 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A TRP 96 HB2 0.263 2.617
4630 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 CG 0.262 3.318
4631 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 2HG1 0.200 2.560
4632 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 H 0.194 2.566
4633 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 CA 0.171 3.409
4634 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 HA 0.167 2.713
4635 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 2HG1 0.075 2.685
4636 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 3HD2 0.068 2.692
4637 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 52 HB3 0.066 2.814
4638 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A TRP 96 CB 0.017 3.563
4639 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LYS 55 HZ1 0.014 2.866
4640 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 C -0.022 3.602
4641 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG1 -0.039 2.919
4642 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG2 -0.053 3.633
4643 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 HB -0.053 2.933
4644 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 N -0.094 3.599
4645 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 HB -0.109 2.719
4646 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A MET 69 O -0.119 3.479
4647 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 3HG1 -0.129 2.739
4648 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 3HD2 -0.130 2.890
4649 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CB -0.136 3.716
4650 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 CB -0.142 3.722
4651 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 HB -0.142 2.752
4652 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A GLY 95 N -0.146 3.651
4653 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 CG1 -0.151 3.611
4654 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 O -0.156 3.516
4655 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 N -0.158 3.543
4656 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 92 O -0.216 3.456
4657 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 3HG1 -0.219 2.829
4658 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG1 -0.219 3.529
4659 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A THR 93 C -0.221 3.801
4660 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 CD2 -0.255 3.715
4661 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 CD2 -0.258 3.718
4662 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ASP 76 OD1 -0.259 3.499
4663 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 C -0.264 3.844
4664 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG2 -0.266 3.146
4665 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 CG1 -0.271 3.731
4666 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG2 -0.280 2.890
4667 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 52 CB -0.282 3.862
4668 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG2 -0.286 2.896
4669 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 HA -0.289 3.049
4670 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ASP 73 OD1 -0.292 3.532
4671 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 N -0.297 3.802
4672 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG1 -0.297 3.877
4673 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG1 -0.299 3.609
4674 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 HB2 -0.302 3.182
4675 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 3HG1 -0.309 3.069
4676 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A TRP 96 CB -0.331 3.791
4677 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 H -0.335 3.215
4678 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CB -0.338 3.648
4679 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LYS 45 HZ3 -0.358 3.118
4680 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 92 HG2 -0.359 2.969
4681 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A THR 93 O -0.359 3.599
4682 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A TRP 96 N -0.383 3.888
4683 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LYS 55 NZ -0.384 3.889
4684 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CB -0.385 3.695
4685 2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ASP 76 OD1 -0.395 3.635
4686
4687
4688
468958 contacts
4690
4691> hbonds :UNL showDist true radius 0.05 log true saveFile
4692> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
4693> WRM-16.hbonds.txt
4694
4695
4696 Finding intermodel H-bonds
4697 Finding intramodel H-bonds
4698 Constraints relaxed by 0.4 angstroms and 20 degrees
4699 Models used:
4700 1 2YSM.pdbqt
4701 2.1 2YSM--WRM-16.result.pdbqt
4702
4703 0 H-bonds
4704 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
4705
4706
4707
47080 hydrogen bonds found
4709
4710> select :UNL
4711
471228 atoms, 31 bonds, 1 residue, 1 model selected
4713
4714> label sel text "Ligand "
4715
4716> label height 1
4717
4718> ~select
4719
4720Nothing selected
4721
4722> 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03
4723> ypos .95
4724
4725> 2dlabels text "2YSM WRM-16 Complex" color gray size 18 xpos .03 ypos .91
4726
4727> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
4728> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
4729> true
4730
4731> select :UNL
4732
473328 atoms, 31 bonds, 1 residue, 1 model selected
4734
4735> view sel
4736
4737> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
4738> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
4739> true
4740
4741> close
4742
4743> wait 5
4744
4745> set bgColor white
4746
4747> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2LNK.pdbqt
4748
4749Chain information for 2LNK.pdbqt #1
4750---
4751Chain | Description
4752A B | No description available
4753C | No description available
4754
4755Opened 2LNK.pdbqt containing 1 structures (3899 atoms, 3931 bonds)
4756
4757> wait 5
4758
4759> hide surfaces
4760
4761> hide atoms
4762
4763> show cartoons
4764
4765> wait 5
4766
4767> addh
4768
4769Summary of feedback from adding hydrogens to 2LNK.pdbqt #1
4770---
4771notes | No usable SEQRES records for 2LNK.pdbqt (#1) chain A; guessing termini
4772instead
4773No usable SEQRES records for 2LNK.pdbqt (#1) chain B; guessing termini instead
4774No usable SEQRES records for 2LNK.pdbqt (#1) chain C; guessing termini instead
4775Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C GLN
47761897
4777Chain-initial residues that are not actual N termini:
4778Chain-final residues that are actual C termini: /A LYS 101, /B LYS 101, /C ALA
47791935
4780Chain-final residues that are not actual C termini:
4781191 hydrogen bonds
47820 hydrogens added
4783
4784
4785> wait 5
4786
4787> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LNK--
4788> WRM-16.result.pdbqt
4789
4790Summary of feedback from opening
4791/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LNK--WRM-16.result.pdbqt
4792---
4793warnings | Ignored bad PDB record found on line 2
4794REMARK VINA RESULT: -7.0 0.000 0.000
4795
4796Ignored bad PDB record found on line 3
4797REMARK 5 active torsions:
4798
4799Ignored bad PDB record found on line 4
4800REMARK status: ('A' for Active; 'I' for Inactive)
4801
4802Ignored bad PDB record found on line 5
4803REMARK 1 A between atoms: C_9 and O_15
4804
4805Ignored bad PDB record found on line 6
4806REMARK 2 A between atoms: C_10 and O_17
4807
4808184 messages similar to the above omitted
4809
4810Opened 2LNK--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
4811bonds)
4812
4813> wait 5
4814
4815> close #2.2-9
4816
4817> wait 5
4818
4819> contacts :UNL radius 0.05 log true saveFile
4820> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
4821> WRM-16.contacts.txt
4822
4823
4824 Allowed overlap: -0.4
4825 H-bond overlap reduction: 0.4
4826 Ignore contacts between atoms separated by 4 bonds or less
4827 Detect intra-residue contacts: False
4828 Detect intra-molecule contacts: True
4829
4830 34 contacts
4831 atom1 atom2 overlap distance
4832 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 0.362 2.518
4833 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CD2 0.342 3.238
4834 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 1HD2 0.261 2.349
4835 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/C THR 1906 2HG2 0.132 2.628
4836 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 0.076 2.534
4837 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A GLU 88 HB2 0.041 2.379
4838 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 ND2 0.005 3.230
4839 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 -0.072 2.952
4840 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 SD -0.095 3.637
4841 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A MET 84 O -0.109 3.049
4842 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A ASN 87 ND2 -0.119 2.804
4843 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A ASN 87 1HD2 -0.126 2.146
4844 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/C THR 1906 CG2 -0.131 3.591
4845 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CD1 -0.159 3.619
4846 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A ASN 87 1HD2 -0.162 2.222
4847 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 -0.219 2.829
4848 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CD1 -0.222 3.682
4849 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CZ -0.228 3.688
4850 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A GLU 88 CB -0.228 3.348
4851 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CD2 -0.254 3.564
4852 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CE2 -0.261 3.841
4853 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 HB3 -0.283 3.043
4854 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 SD -0.288 3.830
4855 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 ND2 -0.291 3.796
4856 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE1 -0.298 3.608
4857 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CD2 -0.300 3.880
4858 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE1 -0.300 3.760
4859 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE1 -0.318 3.778
4860 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 -0.356 2.966
4861 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/B PHE 27 CD2 -0.368 3.488
4862 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CG -0.376 3.836
4863 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE2 -0.386 3.846
4864 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 SD -0.386 3.928
4865 2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 ND2 -0.390 3.895
4866
4867
4868
486934 contacts
4870
4871> hbonds :UNL showDist true radius 0.05 log true saveFile
4872> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
4873> WRM-16.hbonds.txt
4874
4875
4876 Finding intermodel H-bonds
4877 Finding intramodel H-bonds
4878 Constraints relaxed by 0.4 angstroms and 20 degrees
4879 Models used:
4880 1 2LNK.pdbqt
4881 2.1 2LNK--WRM-16.result.pdbqt
4882
4883 0 H-bonds
4884 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
4885
4886
4887
48880 hydrogen bonds found
4889
4890> select :UNL
4891
489228 atoms, 31 bonds, 1 residue, 1 model selected
4893
4894> label sel text "Ligand "
4895
4896> label height 1
4897
4898> ~select
4899
4900Nothing selected
4901
4902> 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03
4903> ypos .95
4904
4905> 2dlabels text "2LNK WRM-16 Complex" color gray size 18 xpos .03 ypos .91
4906
4907> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
4908> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
4909> true
4910
4911> select :UNL
4912
491328 atoms, 31 bonds, 1 residue, 1 model selected
4914
4915> view sel
4916
4917> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
4918> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
4919> true
4920
4921> close
4922
4923> wait 5
4924
4925> set bgColor white
4926
4927> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XUM.pdbqt
4928
4929Chain information for 1XUM.pdbqt #1
4930---
4931Chain | Description
4932A | No description available
4933
4934Opened 1XUM.pdbqt containing 1 structures (2876 atoms, 2908 bonds)
4935
4936> wait 5
4937
4938> hide surfaces
4939
4940> hide atoms
4941
4942> show cartoons
4943
4944> wait 5
4945
4946> addh
4947
4948Summary of feedback from adding hydrogens to 1XUM.pdbqt #1
4949---
4950notes | No usable SEQRES records for 1XUM.pdbqt (#1) chain A; guessing termini
4951instead
4952Chain-initial residues that are actual N termini: /A THR 54
4953Chain-initial residues that are not actual N termini:
4954Chain-final residues that are actual C termini: /A THR 236
4955Chain-final residues that are not actual C termini:
495696 hydrogen bonds
495759 hydrogens added
4958
4959
4960> wait 5
4961
4962> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XUM--
4963> WRM-16.result.pdbqt
4964
4965Summary of feedback from opening
4966/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XUM--WRM-16.result.pdbqt
4967---
4968warnings | Ignored bad PDB record found on line 2
4969REMARK VINA RESULT: -7.8 0.000 0.000
4970
4971Ignored bad PDB record found on line 3
4972REMARK 5 active torsions:
4973
4974Ignored bad PDB record found on line 4
4975REMARK status: ('A' for Active; 'I' for Inactive)
4976
4977Ignored bad PDB record found on line 5
4978REMARK 1 A between atoms: C_9 and O_15
4979
4980Ignored bad PDB record found on line 6
4981REMARK 2 A between atoms: C_10 and O_17
4982
4983184 messages similar to the above omitted
4984
4985Opened 1XUM--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
4986bonds)
4987
4988> wait 5
4989
4990> close #2.2-9
4991
4992> wait 5
4993
4994> contacts :UNL radius 0.05 log true saveFile
4995> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
4996> WRM-16.contacts.txt
4997
4998
4999 Allowed overlap: -0.4
5000 H-bond overlap reduction: 0.4
5001 Ignore contacts between atoms separated by 4 bonds or less
5002 Detect intra-residue contacts: False
5003 Detect intra-molecule contacts: True
5004
5005 50 contacts
5006 atom1 atom2 overlap distance
5007 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 HD2 0.493 2.387
5008 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 HG1 0.216 2.664
5009 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 CD 0.190 3.390
5010 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CE2 0.101 3.359
5011 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A SER 134 HG 0.100 2.660
5012 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 HZ2 0.069 2.691
5013 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 CD 0.018 3.102
5014 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 CE 0.016 3.104
5015 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.001 2.761
5016 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 HD2 -0.002 2.422
5017 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASP 160 OD2 -0.014 2.914
5018 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 185 CB -0.062 3.372
5019 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 HG1 -0.100 2.980
5020 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 OG1 -0.102 3.482
5021 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ASN 110 2HD2 -0.109 2.869
5022 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A GLU 157 OE1 -0.125 3.485
5023 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.126 2.886
5024 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 HD2 -0.128 2.888
5025 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 NZ -0.138 3.523
5026 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 HE2 -0.140 2.900
5027 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CD2 -0.142 3.602
5028 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 185 HB2 -0.156 2.766
5029 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A GLU 157 CD -0.190 3.770
5030 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A TYR 185 HB2 -0.198 2.618
5031 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A TYR 185 CD2 -0.208 3.368
5032 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 HE1 -0.225 2.645
5033 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 HD2 -0.234 2.994
5034 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 CD -0.246 3.706
5035 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.257 3.762
5036 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A SER 134 OG -0.264 3.524
5037 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CD2 -0.267 3.727
5038 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ASN 110 ND2 -0.276 3.661
5039 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 1HG2 -0.283 3.163
5040 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.289 2.899
5041 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASP 160 CG -0.294 3.414
5042 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ASN 186 ND2 -0.305 3.540
5043 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.309 3.694
5044 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A TYR 185 CE2 -0.315 3.475
5045 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A THR 159 OG1 -0.321 2.841
5046 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.331 3.716
5047 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.334 3.719
5048 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 185 CG -0.343 3.653
5049 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 CG2 -0.352 3.932
5050 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.358 3.743
5051 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A THR 159 HG1 -0.360 2.380
5052 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CE2 -0.371 3.831
5053 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A SER 234 HG -0.378 3.258
5054 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 CE -0.381 3.841
5055 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 OG1 -0.387 3.767
5056 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.390 3.150
5057
5058
5059
506050 contacts
5061
5062> hbonds :UNL showDist true radius 0.05 log true saveFile
5063> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
5064> WRM-16.hbonds.txt
5065
5066
5067 Finding intermodel H-bonds
5068 Finding intramodel H-bonds
5069 Constraints relaxed by 0.4 angstroms and 20 degrees
5070 Models used:
5071 1 1XUM.pdbqt
5072 2.1 1XUM--WRM-16.result.pdbqt
5073
5074 2 H-bonds
5075 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5076 1XUM.pdbqt #1/A ASN 186 ND2 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASN 186 1HD2 3.170 2.565
5077 1XUM.pdbqt #1/A ASN 208 ND2 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASN 208 2HD2 3.318 2.547
5078
5079
5080
50812 hydrogen bonds found
5082
5083> select :UNL
5084
508528 atoms, 31 bonds, 1 residue, 1 model selected
5086
5087> label sel text "Ligand "
5088
5089> label height 1
5090
5091> ~select
5092
5093Nothing selected
5094
5095> 2dlabels text "Binding Energy: -7.8 kcal/mol" color red size 18 xpos .03
5096> ypos .95
5097
5098> 2dlabels text "1XUM WRM-16 Complex" color gray size 18 xpos .03 ypos .91
5099
5100> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
5101> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
5102> true
5103
5104> select :UNL
5105
510628 atoms, 31 bonds, 1 residue, 1 model selected
5107
5108> view sel
5109
5110> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
5111> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
5112> true
5113
5114> close
5115
5116> wait 5
5117
5118> set bgColor white
5119
5120> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/6LTH.pdbqt
5121
5122Chain information for 6LTH.pdbqt #1
5123---
5124Chain | Description
5125I | No description available
5126L | No description available
5127M | No description available
5128N | No description available
5129O | No description available
5130P | No description available
5131Q | No description available
5132R | No description available
5133
5134Opened 6LTH.pdbqt containing 1 structures (30136 atoms, 30416 bonds)
5135
5136> wait 5
5137
5138> hide surfaces
5139
5140> hide atoms
5141
5142> show cartoons
5143
5144> wait 5
5145
5146> addh
5147
5148Summary of feedback from adding hydrogens to 6LTH.pdbqt #1
5149---
5150warnings | Not adding hydrogens to /M LYS 199 CD because it is missing heavy-
5151atom bond partners
5152Not adding hydrogens to /M LYS 211 CG because it is missing heavy-atom bond
5153partners
5154notes | No usable SEQRES records for 6LTH.pdbqt (#1) chain I; guessing termini
5155instead
5156No usable SEQRES records for 6LTH.pdbqt (#1) chain L; guessing termini instead
5157No usable SEQRES records for 6LTH.pdbqt (#1) chain M; guessing termini instead
5158No usable SEQRES records for 6LTH.pdbqt (#1) chain N; guessing termini instead
5159No usable SEQRES records for 6LTH.pdbqt (#1) chain O; guessing termini instead
51603 messages similar to the above omitted
5161Chain-initial residues that are actual N termini: /I SER 350, /L ILE 1639, /M
5162SER 7, /N HIS 423, /O HIS 423, /P LYS 125, /Q SER 172, /R GLY 13
5163Chain-initial residues that are not actual N termini: /I LEU 396, /L GLU 1802,
5164/L ILE 1954, /L GLU 2047, /L PRO 2225, /M ASP 78, /M ASP 172, /M GLN 257, /M
5165PRO 332, /N THR 602, /N ASN 671, /N LEU 858, /O THR 598, /O LEU 656, /O ALA
5166867, /P GLN 291, /P THR 399
5167Chain-final residues that are actual C termini: /I LEU 476, /L SER 2285, /M
5168THR 357, /N GLN 952, /O GLN 952, /P GLU 505, /Q LEU 276, /R LYS 82
5169Chain-final residues that are not actual C termini: /I LEU 388, /L ASP 1746,
5170/L LYS 1862, /L LYS 2025, /L GLN 2210, /M SER 67, /M ASP 101, /M PRO 249, /M
5171TYR 326, /N ASP 515, /N ARG 641, /N MET 703, /O GLN 545, /O ASP 651, /O ARG
5172717, /P LYS 177, /P GLU 369
51731386 hydrogen bonds
5174Adding 'H' to /I LEU 396
5175Adding 'H' to /L GLU 1802
5176Adding 'H' to /L ILE 1954
5177Adding 'H' to /L GLU 2047
5178Adding 'H' to /M ASP 78
517910 messages similar to the above omitted
5180/I LEU 388 is not terminus, removing H atom from 'C'
5181/L ASP 1746 is not terminus, removing H atom from 'C'
5182/L LYS 1862 is not terminus, removing H atom from 'C'
5183/L LYS 2025 is not terminus, removing H atom from 'C'
5184/L GLN 2210 is not terminus, removing H atom from 'C'
518512 messages similar to the above omitted
5186-24 hydrogens added
5187
5188
5189> wait 5
5190
5191> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LTH--
5192> WRM-16.result.pdbqt
5193
5194Summary of feedback from opening
5195/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LTH--WRM-16.result.pdbqt
5196---
5197warnings | Ignored bad PDB record found on line 2
5198REMARK VINA RESULT: -8.3 0.000 0.000
5199
5200Ignored bad PDB record found on line 3
5201REMARK 5 active torsions:
5202
5203Ignored bad PDB record found on line 4
5204REMARK status: ('A' for Active; 'I' for Inactive)
5205
5206Ignored bad PDB record found on line 5
5207REMARK 1 A between atoms: C_9 and O_15
5208
5209Ignored bad PDB record found on line 6
5210REMARK 2 A between atoms: C_10 and O_17
5211
5212184 messages similar to the above omitted
5213
5214Opened 6LTH--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
5215bonds)
5216
5217> wait 5
5218
5219> close #2.2-9
5220
5221> wait 5
5222
5223> contacts :UNL radius 0.05 log true saveFile
5224> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
5225> WRM-16.contacts.txt
5226
5227
5228 Allowed overlap: -0.4
5229 H-bond overlap reduction: 0.4
5230 Ignore contacts between atoms separated by 4 bonds or less
5231 Detect intra-residue contacts: False
5232 Detect intra-molecule contacts: True
5233
5234 48 contacts
5235 atom1 atom2 overlap distance
5236 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HG1 0.557 2.203
5237 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CG 0.147 3.313
5238 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PRO 2075 HG2 0.113 2.647
5239 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L PHE 1999 HE1 0.078 2.342
5240 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HG1 0.071 2.689
5241 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L TYR 2076 OH 0.045 3.215
5242 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2070 HA 0.021 2.399
5243 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HA 0.009 2.871
5244 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L TYR 2076 CE1 0.003 3.577
5245 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CA 0.002 3.578
5246 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 HG2 -0.053 2.813
5247 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.064 2.824
5248 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L TYR 2076 CZ -0.085 3.665
5249 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L PRO 2075 HB1 -0.087 2.967
5250 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 CG -0.091 3.551
5251 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L TYR 2076 OH -0.096 3.476
5252 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.114 2.874
5253 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L ASP 2072 HB1 -0.134 3.014
5254 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.135 2.895
5255 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CB -0.137 3.717
5256 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PRO 2075 HG2 -0.165 2.775
5257 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 HG2 -0.175 2.785
5258 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2128 CD -0.176 3.336
5259 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.189 2.949
5260 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 HB2 -0.190 2.950
5261 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L PRO 2075 CB -0.197 3.777
5262 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HB2 -0.207 3.087
5263 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L GLN 2128 OE1 -0.214 3.304
5264 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.215 2.825
5265 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PRO 2075 CG -0.225 3.685
5266 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2070 CA -0.232 3.352
5267 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PHE 1999 HE1 -0.235 2.845
5268 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2070 CD -0.238 3.358
5269 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 CG -0.240 3.700
5270 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 N -0.245 3.750
5271 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L ASP 2072 CB -0.251 3.831
5272 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L PHE 1999 CE1 -0.258 3.378
5273 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CG -0.263 3.723
5274 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L TYR 2076 CZ -0.264 3.724
5275 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L TYR 2076 HH -0.283 3.043
5276 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L GLN 2128 2HE2 -0.292 2.902
5277 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PHE 1999 HE1 -0.313 3.193
5278 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 CG -0.322 3.782
5279 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L GLN 2070 NE2 -0.333 3.568
5280 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.349 2.959
5281 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLU 465 HG2 -0.380 3.140
5282 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2128 OE1 -0.393 3.333
5283 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 CG -0.397 3.857
5284
5285
5286
528748 contacts
5288
5289> hbonds :UNL showDist true radius 0.05 log true saveFile
5290> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
5291> WRM-16.hbonds.txt
5292
5293
5294 Finding intermodel H-bonds
5295 Finding intramodel H-bonds
5296 Constraints relaxed by 0.4 angstroms and 20 degrees
5297 Models used:
5298 1 6LTH.pdbqt
5299 2.1 6LTH--WRM-16.result.pdbqt
5300
5301 1 H-bonds
5302 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5303 6LTH.pdbqt #1/L GLN 2128 NE2 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2128 2HE2 3.227 2.606
5304
5305
5306
53071 hydrogen bonds found
5308
5309> select :UNL
5310
531128 atoms, 31 bonds, 1 residue, 1 model selected
5312
5313> label sel text "Ligand "
5314
5315> label height 1
5316
5317> ~select
5318
5319Nothing selected
5320
5321> 2dlabels text "Binding Energy: -8.3 kcal/mol" color red size 18 xpos .03
5322> ypos .95
5323
5324> 2dlabels text "6LTH WRM-16 Complex" color gray size 18 xpos .03 ypos .91
5325
5326> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
5327> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
5328> true
5329
5330> select :UNL
5331
533228 atoms, 31 bonds, 1 residue, 1 model selected
5333
5334> view sel
5335
5336> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
5337> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
5338> true
5339
5340> close
5341
5342> wait 5
5343
5344> set bgColor white
5345
5346> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3H9R.pdbqt
5347
5348Chain information for 3H9R.pdbqt #1
5349---
5350Chain | Description
5351A | No description available
5352B | No description available
5353
5354Opened 3H9R.pdbqt containing 1 structures (6620 atoms, 6691 bonds)
5355
5356> wait 5
5357
5358> hide surfaces
5359
5360> hide atoms
5361
5362> show cartoons
5363
5364> wait 5
5365
5366> addh
5367
5368Summary of feedback from adding hydrogens to 3H9R.pdbqt #1
5369---
5370warnings | Not adding hydrogens to /A ARG 218 CD because it is missing heavy-
5371atom bond partners
5372Not adding hydrogens to /A SER 276 CB because it is missing heavy-atom bond
5373partners
5374Not adding hydrogens to /A ASP 499 CB because it is missing heavy-atom bond
5375partners
5376Not adding hydrogens to /B ARG 14 CB because it is missing heavy-atom bond
5377partners
5378notes | No usable SEQRES records for 3H9R.pdbqt (#1) chain A; guessing termini
5379instead
5380No usable SEQRES records for 3H9R.pdbqt (#1) chain B; guessing termini instead
5381Chain-initial residues that are actual N termini: /A THR 172, /B GLY 2
5382Chain-initial residues that are not actual N termini: /A SER 276, /A ARG 375
5383Chain-final residues that are actual C termini: /A ASP 499, /B GLU 108
5384Chain-final residues that are not actual C termini: /A SER 272, /A HIS 361
5385360 hydrogen bonds
5386Adding 'H' to /A SER 276
5387Adding 'H' to /A ARG 375
5388/A SER 272 is not terminus, removing H atom from 'C'
5389/A HIS 361 is not terminus, removing H atom from 'C'
53907 hydrogens added
5391
5392
5393> wait 5
5394
5395> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3H9R--
5396> WRM-16.result.pdbqt
5397
5398Summary of feedback from opening
5399/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3H9R--WRM-16.result.pdbqt
5400---
5401warnings | Ignored bad PDB record found on line 2
5402REMARK VINA RESULT: -10.1 0.000 0.000
5403
5404Ignored bad PDB record found on line 3
5405REMARK 5 active torsions:
5406
5407Ignored bad PDB record found on line 4
5408REMARK status: ('A' for Active; 'I' for Inactive)
5409
5410Ignored bad PDB record found on line 5
5411REMARK 1 A between atoms: C_9 and O_15
5412
5413Ignored bad PDB record found on line 6
5414REMARK 2 A between atoms: C_10 and O_17
5415
5416184 messages similar to the above omitted
5417
5418Opened 3H9R--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
5419bonds)
5420
5421> wait 5
5422
5423> close #2.2-9
5424
5425> wait 5
5426
5427> contacts :UNL radius 0.05 log true saveFile
5428> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
5429> WRM-16.contacts.txt
5430
5431
5432 Allowed overlap: -0.4
5433 H-bond overlap reduction: 0.4
5434 Ignore contacts between atoms separated by 4 bonds or less
5435 Detect intra-residue contacts: False
5436 Detect intra-molecule contacts: True
5437
5438 56 contacts
5439 atom1 atom2 overlap distance
5440 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A GLY 215 HA2 0.237 2.643
5441 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A LYS 340 HE1 0.199 2.681
5442 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A SER 290 HG 0.131 2.629
5443 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HG1 0.091 2.669
5444 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 OH 0.084 3.296
5445 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 2HG1 0.026 2.734
5446 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 3HD2 -0.001 2.611
5447 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 CB -0.040 3.500
5448 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HE1 -0.051 2.811
5449 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HE1 -0.053 2.663
5450 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A GLY 215 CA -0.076 3.656
5451 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 2HD1 -0.077 2.687
5452 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 O -0.104 3.344
5453 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HH -0.112 2.992
5454 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 214 1HG2 -0.136 2.896
5455 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 O -0.146 3.506
5456 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HH -0.154 2.914
5457 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 2HG1 -0.157 2.767
5458 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 3HD2 -0.158 2.768
5459 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A ASP 293 OD2 -0.168 3.528
5460 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 CZ -0.169 3.749
5461 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 214 CG2 -0.171 3.631
5462 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 285 CD1 -0.171 3.631
5463 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A SER 290 OG -0.174 3.434
5464 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 CE -0.180 3.640
5465 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 3HD2 -0.205 2.815
5466 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A LYS 340 CE -0.206 3.786
5467 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HE2 -0.256 3.016
5468 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 CE2 -0.259 3.839
5469 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 CG -0.261 3.721
5470 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O 3H9R.pdbqt #1/A LEU 343 2HD1 -0.276 2.736
5471 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 CD2 -0.279 3.589
5472 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O 3H9R.pdbqt #1/A ALA 353 HB1 -0.284 2.704
5473 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HG1 -0.287 3.047
5474 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HG1 -0.287 2.897
5475 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB1 -0.289 3.049
5476 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB2 -0.297 3.177
5477 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB1 -0.298 3.058
5478 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 CD2 -0.307 3.617
5479 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A TYR 292 CD2 -0.308 3.888
5480 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 3HG2 -0.317 2.927
5481 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB2 -0.319 3.079
5482 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 285 CE1 -0.325 3.785
5483 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A TYR 292 HD2 -0.326 3.206
5484 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 CB -0.326 3.786
5485 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 2HG1 -0.350 3.110
5486 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 CG1 -0.350 3.810
5487 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 CE2 -0.367 3.677
5488 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 CE -0.368 3.678
5489 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HE2 -0.371 2.981
5490 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 O -0.374 3.464
5491 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 CB -0.376 3.956
5492 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 263 1HD2 -0.382 3.262
5493 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O 3H9R.pdbqt #1/A LEU 263 CD2 -0.384 3.544
5494 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 285 HD1 -0.388 3.148
5495 3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 CG1 -0.390 3.970
5496
5497
5498
549956 contacts
5500
5501> hbonds :UNL showDist true radius 0.05 log true saveFile
5502> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
5503> WRM-16.hbonds.txt
5504
5505
5506 Finding intermodel H-bonds
5507 Finding intramodel H-bonds
5508 Constraints relaxed by 0.4 angstroms and 20 degrees
5509 Models used:
5510 1 3H9R.pdbqt
5511 2.1 3H9R--WRM-16.result.pdbqt
5512
5513 0 H-bonds
5514 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5515
5516
5517
55180 hydrogen bonds found
5519
5520> select :UNL
5521
552228 atoms, 31 bonds, 1 residue, 1 model selected
5523
5524> label sel text "Ligand "
5525
5526> label height 1
5527
5528> ~select
5529
5530Nothing selected
5531
5532> 2dlabels text "Binding Energy: -10.1 kcal/mol" color red size 18 xpos .03
5533> ypos .95
5534
5535> 2dlabels text "3H9R WRM-16 Complex" color gray size 18 xpos .03 ypos .91
5536
5537> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
5538> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
5539> true
5540
5541> select :UNL
5542
554328 atoms, 31 bonds, 1 residue, 1 model selected
5544
5545> view sel
5546
5547> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
5548> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
5549> true
5550
5551> close
5552
5553> wait 5
5554
5555> set bgColor white
5556
5557> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1A5E.pdbqt
5558
5559Chain information for 1A5E.pdbqt #1
5560---
5561Chain | Description
5562A | No description available
5563
5564Opened 1A5E.pdbqt containing 1 structures (2306 atoms, 2328 bonds)
5565
5566> wait 5
5567
5568> hide surfaces
5569
5570> hide atoms
5571
5572> show cartoons
5573
5574> wait 5
5575
5576> addh
5577
5578Summary of feedback from adding hydrogens to 1A5E.pdbqt #1
5579---
5580notes | No usable SEQRES records for 1A5E.pdbqt (#1) chain A; guessing termini
5581instead
5582Chain-initial residues that are actual N termini: /A MET 1
5583Chain-initial residues that are not actual N termini:
5584Chain-final residues that are actual C termini: /A ASP 156
5585Chain-final residues that are not actual C termini:
558664 hydrogen bonds
55870 hydrogens added
5588
5589
5590> wait 5
5591
5592> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1A5E--
5593> WRM-16.result.pdbqt
5594
5595Summary of feedback from opening
5596/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1A5E--WRM-16.result.pdbqt
5597---
5598warnings | Ignored bad PDB record found on line 2
5599REMARK VINA RESULT: -6.6 0.000 0.000
5600
5601Ignored bad PDB record found on line 3
5602REMARK 5 active torsions:
5603
5604Ignored bad PDB record found on line 4
5605REMARK status: ('A' for Active; 'I' for Inactive)
5606
5607Ignored bad PDB record found on line 5
5608REMARK 1 A between atoms: C_9 and O_15
5609
5610Ignored bad PDB record found on line 6
5611REMARK 2 A between atoms: C_10 and O_17
5612
5613184 messages similar to the above omitted
5614
5615Opened 1A5E--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
5616bonds)
5617
5618> wait 5
5619
5620> close #2.2-9
5621
5622> wait 5
5623
5624> contacts :UNL radius 0.05 log true saveFile
5625> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
5626> WRM-16.contacts.txt
5627
5628
5629 Allowed overlap: -0.4
5630 H-bond overlap reduction: 0.4
5631 Ignore contacts between atoms separated by 4 bonds or less
5632 Detect intra-residue contacts: False
5633 Detect intra-molecule contacts: True
5634
5635 45 contacts
5636 atom1 atom2 overlap distance
5637 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 1HH1 0.185 2.695
5638 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ARG 112 1HH1 0.171 1.889
5639 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A GLY 111 HA3 0.148 2.732
5640 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 HD3 0.134 2.626
5641 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A LEU 117 2HD1 0.063 2.817
5642 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A GLY 111 CA 0.033 3.547
5643 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 NH1 0.030 3.475
5644 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CD2 -0.013 3.593
5645 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A LEU 117 CD1 -0.018 3.598
5646 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.022 2.782
5647 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CG -0.036 3.616
5648 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A PRO 151 HD3 -0.038 2.918
5649 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.064 2.824
5650 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CH2 -0.074 3.384
5651 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.085 2.845
5652 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ARG 112 NH1 -0.090 2.775
5653 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A LEU 117 3HD1 -0.118 2.538
5654 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 87 NH2 -0.119 3.624
5655 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.131 2.891
5656 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A PRO 151 CD -0.159 3.739
5657 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.161 2.771
5658 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CB -0.174 3.634
5659 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ASP 108 OD2 -0.193 3.133
5660 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A GLY 111 N -0.213 3.598
5661 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CH2 -0.218 3.678
5662 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CB -0.221 3.681
5663 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A GLY 111 N -0.227 3.732
5664 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 CD -0.234 3.694
5665 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CZ3 -0.255 3.565
5666 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CD1 -0.273 3.853
5667 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A LEU 117 CD1 -0.275 3.395
5668 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CE2 -0.277 3.857
5669 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CZ3 -0.277 3.587
5670 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CH2 -0.289 3.599
5671 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 HD3 -0.299 3.059
5672 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.303 2.913
5673 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A GLY 111 C -0.323 3.783
5674 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 1HH1 -0.339 2.949
5675 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A TRP 110 C -0.352 3.932
5676 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 HB2 -0.359 3.119
5677 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 46 NH2 -0.361 3.746
5678 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 87 2HH2 -0.361 3.241
5679 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CD1 -0.370 3.830
5680 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CB -0.386 3.846
5681 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 1HH1 -0.399 3.009
5682
5683
5684
568545 contacts
5686
5687> hbonds :UNL showDist true radius 0.05 log true saveFile
5688> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
5689> WRM-16.hbonds.txt
5690
5691
5692 Finding intermodel H-bonds
5693 Finding intramodel H-bonds
5694 Constraints relaxed by 0.4 angstroms and 20 degrees
5695 Models used:
5696 1 1A5E.pdbqt
5697 2.1 1A5E--WRM-16.result.pdbqt
5698
5699 1 H-bonds
5700 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5701 1A5E.pdbqt #1/A ARG 112 NH1 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ARG 112 1HH1 2.775 1.889
5702
5703
5704
57051 hydrogen bonds found
5706
5707> select :UNL
5708
570928 atoms, 31 bonds, 1 residue, 1 model selected
5710
5711> label sel text "Ligand "
5712
5713> label height 1
5714
5715> ~select
5716
5717Nothing selected
5718
5719> 2dlabels text "Binding Energy: -6.6 kcal/mol" color red size 18 xpos .03
5720> ypos .95
5721
5722> 2dlabels text "1A5E WRM-16 Complex" color gray size 18 xpos .03 ypos .91
5723
5724> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
5725> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
5726> true
5727
5728> select :UNL
5729
573028 atoms, 31 bonds, 1 residue, 1 model selected
5731
5732> view sel
5733
5734> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
5735> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
5736> true
5737
5738> close
5739
5740> wait 5
5741
5742> set bgColor white
5743
5744> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1ES7.pdbqt
5745
5746Chain information for 1ES7.pdbqt #1
5747---
5748Chain | Description
5749A C | No description available
5750B | No description available
5751D | No description available
5752
5753Opened 1ES7.pdbqt containing 1 structures (5745 atoms, 5815 bonds)
5754
5755> wait 5
5756
5757> hide surfaces
5758
5759> hide atoms
5760
5761> show cartoons
5762
5763> wait 5
5764
5765> addh
5766
5767Summary of feedback from adding hydrogens to 1ES7.pdbqt #1
5768---
5769notes | No usable SEQRES records for 1ES7.pdbqt (#1) chain A; guessing termini
5770instead
5771No usable SEQRES records for 1ES7.pdbqt (#1) chain B; guessing termini instead
5772No usable SEQRES records for 1ES7.pdbqt (#1) chain C; guessing termini instead
5773No usable SEQRES records for 1ES7.pdbqt (#1) chain D; guessing termini instead
5774Chain-initial residues that are actual N termini: /A LYS 11, /B THR 232, /C
5775LYS 511, /D THR 732
5776Chain-initial residues that are not actual N termini: /B GLU 270, /D GLU 770
5777Chain-final residues that are actual C termini: /A ARG 114, /B PRO 317, /C ARG
5778614, /D ILE 820
5779Chain-final residues that are not actual C termini: /B ASP 266, /D ASP 766
5780270 hydrogen bonds
5781Adding 'H' to /B GLU 270
5782Adding 'H' to /D GLU 770
5783/B ASP 266 is not terminus, removing H atom from 'C'
5784/D ASP 766 is not terminus, removing H atom from 'C'
578528 hydrogens added
5786
5787
5788> wait 5
5789
5790> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1ES7--
5791> WRM-16.result.pdbqt
5792
5793Summary of feedback from opening
5794/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1ES7--WRM-16.result.pdbqt
5795---
5796warnings | Ignored bad PDB record found on line 2
5797REMARK VINA RESULT: -7.5 0.000 0.000
5798
5799Ignored bad PDB record found on line 3
5800REMARK 5 active torsions:
5801
5802Ignored bad PDB record found on line 4
5803REMARK status: ('A' for Active; 'I' for Inactive)
5804
5805Ignored bad PDB record found on line 5
5806REMARK 1 A between atoms: C_9 and O_15
5807
5808Ignored bad PDB record found on line 6
5809REMARK 2 A between atoms: C_10 and O_17
5810
5811184 messages similar to the above omitted
5812
5813Opened 1ES7--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
5814bonds)
5815
5816> wait 5
5817
5818> close #2.2-9
5819
5820> wait 5
5821
5822> contacts :UNL radius 0.05 log true saveFile
5823> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
5824> WRM-16.contacts.txt
5825
5826
5827 Allowed overlap: -0.4
5828 H-bond overlap reduction: 0.4
5829 Ignore contacts between atoms separated by 4 bonds or less
5830 Detect intra-residue contacts: False
5831 Detect intra-molecule contacts: True
5832
5833 46 contacts
5834 atom1 atom2 overlap distance
5835 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 HN 0.266 2.614
5836 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ARG 16 HN 0.165 1.855
5837 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B PRO 245 HB2 0.115 2.645
5838 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 ND1 0.101 3.404
5839 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HD1 0.099 2.781
5840 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 HN 0.038 2.022
5841 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 HB2 -0.021 2.781
5842 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.077 2.687
5843 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 N -0.107 3.612
5844 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 1HD2 -0.114 2.134
5845 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B PRO 245 CB -0.134 3.594
5846 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 HN -0.134 2.744
5847 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ASN 56 1HD2 -0.156 2.766
5848 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ARG 16 N -0.177 2.822
5849 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 HN -0.181 2.791
5850 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 CB -0.198 3.658
5851 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 HN -0.206 2.966
5852 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A GLY 110 HA1 -0.216 2.636
5853 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 OD1 -0.230 3.470
5854 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 OD2 -0.233 3.473
5855 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.234 2.994
5856 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 CB -0.239 3.699
5857 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 HB2 -0.244 3.004
5858 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.248 3.128
5859 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 HB2 -0.253 3.013
5860 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 O -0.274 3.364
5861 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A GLY 110 CA -0.280 3.400
5862 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 O -0.305 3.205
5863 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 CB -0.311 3.771
5864 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 OD1 -0.316 3.556
5865 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A LYS 15 CA -0.326 3.446
5866 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 O -0.327 3.567
5867 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 2HD2 -0.328 2.388
5868 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A LYS 15 HA -0.330 2.750
5869 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 OD2 -0.331 3.571
5870 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 CB -0.338 3.648
5871 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 N -0.338 3.573
5872 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 N -0.339 3.024
5873 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 O -0.361 3.301
5874 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ASN 56 ND2 -0.363 3.598
5875 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 N -0.363 3.748
5876 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 ND2 -0.369 3.014
5877 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 CG -0.374 3.834
5878 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.375 2.985
5879 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 ND2 -0.381 3.066
5880 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 HN -0.394 3.274
5881
5882
5883
588446 contacts
5885
5886> hbonds :UNL showDist true radius 0.05 log true saveFile
5887> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
5888> WRM-16.hbonds.txt
5889
5890
5891 Finding intermodel H-bonds
5892 Finding intramodel H-bonds
5893 Constraints relaxed by 0.4 angstroms and 20 degrees
5894 Models used:
5895 1 1ES7.pdbqt
5896 2.1 1ES7--WRM-16.result.pdbqt
5897
5898 4 H-bonds
5899 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5900 1ES7.pdbqt #1/A ARG 16 N 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ARG 16 HN 2.822 1.855
5901 1ES7.pdbqt #1/A ASN 56 ND2 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 1HD2 3.014 2.134
5902 1ES7.pdbqt #1/A ASN 56 ND2 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 2HD2 3.066 2.388
5903 1ES7.pdbqt #1/A CYS 111 N 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 HN 3.024 2.022
5904
5905
5906
59074 hydrogen bonds found
5908
5909> select :UNL
5910
591128 atoms, 31 bonds, 1 residue, 1 model selected
5912
5913> label sel text "Ligand "
5914
5915> label height 1
5916
5917> ~select
5918
5919Nothing selected
5920
5921> 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03
5922> ypos .95
5923
5924> 2dlabels text "1ES7 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
5925
5926> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
5927> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
5928> true
5929
5930> select :UNL
5931
593228 atoms, 31 bonds, 1 residue, 1 model selected
5933
5934> view sel
5935
5936> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
5937> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
5938> true
5939
5940> close
5941
5942> wait 5
5943
5944> set bgColor white
5945
5946> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3TGX.pdbqt
5947
5948Chain information for 3TGX.pdbqt #1
5949---
5950Chain | Description
5951A M O | No description available
5952B | No description available
5953C G I K | No description available
5954D | No description available
5955E | No description available
5956F | No description available
5957H | No description available
5958J | No description available
5959L | No description available
5960N | No description available
5961P | No description available
5962
5963Opened 3TGX.pdbqt containing 1 structures (41174 atoms, 41719 bonds)
5964
5965> wait 5
5966
5967> hide surfaces
5968
5969> hide atoms
5970
5971> show cartoons
5972
5973> wait 5
5974
5975> addh
5976
5977Summary of feedback from adding hydrogens to 3TGX.pdbqt #1
5978---
5979warning | Not adding hydrogens to /J ARG 126 CB because it is missing heavy-
5980atom bond partners
5981notes | No usable SEQRES records for 3TGX.pdbqt (#1) chain A; guessing termini
5982instead
5983No usable SEQRES records for 3TGX.pdbqt (#1) chain B; guessing termini instead
5984No usable SEQRES records for 3TGX.pdbqt (#1) chain C; guessing termini instead
5985No usable SEQRES records for 3TGX.pdbqt (#1) chain D; guessing termini instead
5986No usable SEQRES records for 3TGX.pdbqt (#1) chain E; guessing termini instead
598711 messages similar to the above omitted
5988Chain-initial residues that are actual N termini: /A CYS 1, /B GLY 2, /C CYS
59891, /D GLY 2, /E CYS 1, /F GLY 2, /G CYS 1, /H ASP 4, /I CYS 1, /J GLY 2, /K
5990CYS 1, /L ASP 4, /M CYS 1, /N ASP 4, /O CYS 1, /P ASP 4
5991Chain-initial residues that are not actual N termini: /B HIS 89, /D LEU 91, /F
5992THR 92, /H GLN 87, /J LEU 91, /L LEU 91, /N THR 92, /P THR 92
5993Chain-final residues that are actual C termini: /A SER 208, /B LEU 123, /C GLU
5994209, /D LEU 123, /E GLN 207, /F LEU 123, /G GLU 209, /H LEU 123, /I GLU 209,
5995/J ARG 126, /K GLU 209, /L HIS 122, /M SER 208, /N HIS 120, /O SER 208, /P LEU
5996123
5997Chain-final residues that are not actual C termini: /B THR 81, /D ARG 85, /F
5998ASN 82, /H ASN 82, /J THR 81, /L THR 81, /N THR 81, /P THR 81
59991792 hydrogen bonds
6000Adding 'H' to /B HIS 89
6001Adding 'H' to /D LEU 91
6002Adding 'H' to /F THR 92
6003Adding 'H' to /H GLN 87
6004Adding 'H' to /J LEU 91
60053 messages similar to the above omitted
6006/B THR 81 is not terminus, removing H atom from 'C'
6007/D ARG 85 is not terminus, removing H atom from 'C'
6008/F ASN 82 is not terminus, removing H atom from 'C'
6009/H ASN 82 is not terminus, removing H atom from 'C'
6010/J THR 81 is not terminus, removing H atom from 'C'
60113 messages similar to the above omitted
601280 hydrogens added
6013
6014
6015> wait 5
6016
6017> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3TGX--
6018> WRM-16.result.pdbqt
6019
6020Summary of feedback from opening
6021/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3TGX--WRM-16.result.pdbqt
6022---
6023warnings | Ignored bad PDB record found on line 2
6024REMARK VINA RESULT: -8.5 0.000 0.000
6025
6026Ignored bad PDB record found on line 3
6027REMARK 5 active torsions:
6028
6029Ignored bad PDB record found on line 4
6030REMARK status: ('A' for Active; 'I' for Inactive)
6031
6032Ignored bad PDB record found on line 5
6033REMARK 1 A between atoms: C_9 and O_15
6034
6035Ignored bad PDB record found on line 6
6036REMARK 2 A between atoms: C_10 and O_17
6037
6038184 messages similar to the above omitted
6039
6040Opened 3TGX--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
6041bonds)
6042
6043> wait 5
6044
6045> close #2.2-9
6046
6047> wait 5
6048
6049> contacts :UNL radius 0.05 log true saveFile
6050> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
6051> WRM-16.contacts.txt
6052
6053
6054 Allowed overlap: -0.4
6055 H-bond overlap reduction: 0.4
6056 Ignore contacts between atoms separated by 4 bonds or less
6057 Detect intra-residue contacts: False
6058 Detect intra-molecule contacts: True
6059
6060 84 contacts
6061 atom1 atom2 overlap distance
6062 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 1HD2 0.702 2.058
6063 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M ASN 22 2HD2 0.553 2.327
6064 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 HB2 0.512 2.368
6065 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 ND2 0.484 2.901
6066 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASP 81 OD1 0.349 3.011
6067 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 HH 0.297 2.463
6068 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/E ALA 127 HB1 0.227 2.533
6069 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 1HE2 0.207 2.403
6070 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HG1 0.181 2.579
6071 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CB 0.180 3.400
6072 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 OH 0.166 3.094
6073 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M ASN 22 ND2 0.163 3.342
6074 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 CB 0.149 3.431
6075 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 CD1 0.133 3.447
6076 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 NE 0.132 3.373
6077 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB1 0.131 2.749
6078 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 HD1 0.115 2.765
6079 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 CB 0.110 3.470
6080 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 0.094 2.786
6081 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 CG1 0.089 3.491
6082 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 HN 0.077 2.683
6083 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/E ALA 127 CB 0.016 3.444
6084 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 NE1 0.005 3.500
6085 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 2HG1 0.001 2.879
6086 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.001 2.611
6087 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/E ALA 127 CB -0.006 3.586
6088 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASP 81 OD1 -0.008 3.248
6089 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 1HG1 -0.043 2.923
6090 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 HN -0.056 2.816
6091 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 HE1 -0.056 2.936
6092 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M ASN 22 ND2 -0.057 3.292
6093 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 1HE2 -0.067 2.127
6094 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CG -0.098 3.678
6095 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 NE2 -0.104 3.339
6096 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 ND2 -0.107 3.612
6097 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 HD2 -0.112 2.872
6098 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB1 -0.119 2.879
6099 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB1 -0.134 3.014
6100 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/E ALA 127 HB1 -0.143 3.023
6101 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.158 2.768
6102 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 CG -0.159 3.619
6103 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HG1 -0.159 3.039
6104 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/F ASN 62 HB2 -0.163 2.623
6105 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 1HD2 -0.178 2.938
6106 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 ND2 -0.185 3.690
6107 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CG -0.188 3.648
6108 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 N -0.192 3.577
6109 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 -0.208 2.818
6110 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.228 3.108
6111 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB2 -0.235 3.115
6112 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.240 3.000
6113 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 CE1 -0.248 3.708
6114 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 HH -0.249 3.009
6115 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 CG -0.260 3.840
6116 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 CB -0.262 3.842
6117 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 CD -0.265 3.845
6118 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 CZ -0.271 3.851
6119 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 N -0.274 3.779
6120 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB1 -0.281 3.161
6121 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 HE -0.296 3.176
6122 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB2 -0.296 3.176
6123 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 ND2 -0.298 3.533
6124 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/A ASP 81 OD1 -0.308 3.248
6125 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/E ALA 127 HB2 -0.313 3.193
6126 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 -0.319 2.929
6127 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 OH -0.336 3.596
6128 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 CD -0.339 3.799
6129 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 -0.343 2.953
6130 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 CB -0.346 3.806
6131 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HG1 -0.347 3.107
6132 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 CD2 -0.354 3.814
6133 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 HB2 -0.356 2.816
6134 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 HB2 -0.357 3.117
6135 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 ND2 -0.361 3.746
6136 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.361 3.121
6137 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 CG -0.362 3.522
6138 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 ND2 -0.368 3.603
6139 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 1HD2 -0.370 3.250
6140 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CB -0.370 3.680
6141 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 1HE2 -0.388 3.268
6142 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 NE2 -0.389 3.774
6143 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 HB2 -0.390 3.150
6144 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 ND1 -0.394 3.779
6145 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/A ASN 22 ND2 -0.395 3.080
6146
6147
6148
614984 contacts
6150
6151> hbonds :UNL showDist true radius 0.05 log true saveFile
6152> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
6153> WRM-16.hbonds.txt
6154
6155
6156 Finding intermodel H-bonds
6157 Finding intramodel H-bonds
6158 Constraints relaxed by 0.4 angstroms and 20 degrees
6159 Models used:
6160 1 3TGX.pdbqt
6161 2.1 3TGX--WRM-16.result.pdbqt
6162
6163 1 H-bonds
6164 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6165 3TGX.pdbqt #1/M GLN 82 NE2 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 1HE2 3.121 2.127
6166
6167
6168
61691 hydrogen bonds found
6170
6171> select :UNL
6172
617328 atoms, 31 bonds, 1 residue, 1 model selected
6174
6175> label sel text "Ligand "
6176
6177> label height 1
6178
6179> ~select
6180
6181Nothing selected
6182
6183> 2dlabels text "Binding Energy: -8.5 kcal/mol" color red size 18 xpos .03
6184> ypos .95
6185
6186> 2dlabels text "3TGX WRM-16 Complex" color gray size 18 xpos .03 ypos .91
6187
6188> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
6189> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
6190> true
6191
6192> select :UNL
6193
619428 atoms, 31 bonds, 1 residue, 1 model selected
6195
6196> view sel
6197
6198> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
6199> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
6200> true
6201
6202> close
6203
6204> wait 5
6205
6206> set bgColor white
6207
6208> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/4JUP.pdbqt
6209
6210Chain information for 4JUP.pdbqt #1
6211---
6212Chain | Description
6213A B | No description available
6214
6215Opened 4JUP.pdbqt containing 1 structures (2664 atoms, 2690 bonds)
6216
6217> wait 5
6218
6219> hide surfaces
6220
6221> hide atoms
6222
6223> show cartoons
6224
6225> wait 5
6226
6227> addh
6228
6229Summary of feedback from adding hydrogens to 4JUP.pdbqt #1
6230---
6231notes | No usable SEQRES records for 4JUP.pdbqt (#1) chain A; guessing termini
6232instead
6233No usable SEQRES records for 4JUP.pdbqt (#1) chain B; guessing termini instead
6234Chain-initial residues that are actual N termini: /A LEU 22, /B LEU 22
6235Chain-initial residues that are not actual N termini: /A ASN 71, /B ASN 71
6236Chain-final residues that are actual C termini: /A GLY 108, /B GLY 108
6237Chain-final residues that are not actual C termini: /A ALA 63, /B ALA 63
6238116 hydrogen bonds
6239Adding 'H' to /A ASN 71
6240Adding 'H' to /B ASN 71
6241/A ALA 63 is not terminus, removing H atom from 'C'
6242/B ALA 63 is not terminus, removing H atom from 'C'
6243-2 hydrogens added
6244
6245
6246> wait 5
6247
6248> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/4JUP--
6249> WRM-16.result.pdbqt
6250
6251Summary of feedback from opening
6252/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/4JUP--WRM-16.result.pdbqt
6253---
6254warnings | Ignored bad PDB record found on line 2
6255REMARK VINA RESULT: -7.9 0.000 0.000
6256
6257Ignored bad PDB record found on line 3
6258REMARK 5 active torsions:
6259
6260Ignored bad PDB record found on line 4
6261REMARK status: ('A' for Active; 'I' for Inactive)
6262
6263Ignored bad PDB record found on line 5
6264REMARK 1 A between atoms: C_9 and O_15
6265
6266Ignored bad PDB record found on line 6
6267REMARK 2 A between atoms: C_10 and O_17
6268
6269184 messages similar to the above omitted
6270
6271Opened 4JUP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
6272bonds)
6273
6274> wait 5
6275
6276> close #2.2-9
6277
6278> wait 5
6279
6280> contacts :UNL radius 0.05 log true saveFile
6281> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
6282> WRM-16.contacts.txt
6283
6284
6285 Allowed overlap: -0.4
6286 H-bond overlap reduction: 0.4
6287 Ignore contacts between atoms separated by 4 bonds or less
6288 Detect intra-residue contacts: False
6289 Detect intra-molecule contacts: True
6290
6291 77 contacts
6292 atom1 atom2 overlap distance
6293 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 HA 0.493 1.967
6294 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 HA 0.445 2.315
6295 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 HB1 0.307 2.573
6296 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG 0.303 2.457
6297 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 O 0.286 3.074
6298 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 HB1 0.217 2.663
6299 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 HD2 0.197 2.683
6300 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 CA 0.183 2.977
6301 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 HG2 0.161 2.599
6302 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B HIS 31 CE1 0.142 3.018
6303 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG 0.130 2.630
6304 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH2 0.110 2.770
6305 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 CB 0.083 3.497
6306 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ILE 79 HA 0.074 2.686
6307 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 CA 0.055 3.405
6308 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 CG 0.047 3.413
6309 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 2HH2 0.027 1.993
6310 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A THR 82 HG1 -0.010 2.770
6311 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 HB1 -0.017 2.777
6312 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG -0.018 2.778
6313 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH1 -0.024 2.634
6314 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 NH2 -0.029 3.534
6315 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CB -0.049 3.629
6316 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 OG -0.079 3.339
6317 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A THR 82 HG1 -0.087 2.697
6318 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A THR 82 HG1 -0.105 2.985
6319 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 CD -0.111 3.691
6320 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ASN 71 HA -0.119 2.999
6321 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD2 -0.153 3.243
6322 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 NH2 -0.159 2.804
6323 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD2 -0.165 3.255
6324 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A THR 82 1HG2 -0.181 3.061
6325 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A THR 82 OG1 -0.189 3.449
6326 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 HA -0.191 2.951
6327 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 CE1 -0.199 3.779
6328 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 30 HD2 -0.203 2.963
6329 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 30 CD -0.205 3.665
6330 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ILE 79 1HG1 -0.205 2.965
6331 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH2 -0.206 2.816
6332 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 NH1 -0.210 3.445
6333 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 HG2 -0.213 2.973
6334 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASN 71 2HD2 -0.213 3.093
6335 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ILE 79 CA -0.215 3.675
6336 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HB1 -0.220 3.100
6337 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A ILE 79 CG1 -0.228 3.808
6338 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 OG -0.243 3.503
6339 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CG -0.244 3.824
6340 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH1 -0.246 2.856
6341 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A ILE 79 1HG1 -0.248 3.128
6342 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD2 -0.258 3.498
6343 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ASN 71 OD1 -0.262 3.622
6344 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 CB -0.272 3.732
6345 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 HB2 -0.297 2.717
6346 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 CB -0.302 3.422
6347 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B HIS 31 ND1 -0.304 2.989
6348 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASN 71 ND2 -0.305 3.810
6349 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 C -0.306 3.886
6350 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 CG -0.306 3.426
6351 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CB -0.308 3.768
6352 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 C -0.314 3.774
6353 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 OG -0.315 3.575
6354 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 CG -0.316 3.776
6355 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 C -0.326 3.786
6356 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG -0.329 3.089
6357 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 ND1 -0.343 3.848
6358 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD1 -0.346 3.706
6359 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 HG1 -0.355 3.115
6360 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 NH2 -0.360 3.595
6361 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 CA -0.362 3.942
6362 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CG -0.365 3.675
6363 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HB1 -0.370 3.130
6364 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ASN 71 HA -0.375 2.985
6365 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 CZ -0.378 3.498
6366 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 30 NH1 -0.384 3.769
6367 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 C -0.385 3.845
6368 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 CB -0.388 3.698
6369 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH1 -0.396 3.276
6370
6371
6372
637377 contacts
6374
6375> hbonds :UNL showDist true radius 0.05 log true saveFile
6376> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
6377> WRM-16.hbonds.txt
6378
6379
6380 Finding intermodel H-bonds
6381 Finding intramodel H-bonds
6382 Constraints relaxed by 0.4 angstroms and 20 degrees
6383 Models used:
6384 1 4JUP.pdbqt
6385 2.1 4JUP--WRM-16.result.pdbqt
6386
6387 1 H-bonds
6388 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6389 4JUP.pdbqt #1/A ARG 75 NH2 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 2HH2 2.804 1.993
6390
6391
6392
63931 hydrogen bonds found
6394
6395> select :UNL
6396
639728 atoms, 31 bonds, 1 residue, 1 model selected
6398
6399> label sel text "Ligand "
6400
6401> label height 1
6402
6403> ~select
6404
6405Nothing selected
6406
6407> 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
6408> ypos .95
6409
6410> 2dlabels text "4JUP WRM-16 Complex" color gray size 18 xpos .03 ypos .91
6411
6412> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
6413> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
6414> true
6415
6416> select :UNL
6417
641828 atoms, 31 bonds, 1 residue, 1 model selected
6419
6420> view sel
6421
6422> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
6423> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
6424> true
6425
6426> close
6427
6428> wait 5
6429
6430> set bgColor white
6431
6432> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1FLI.pdbqt
6433
6434Chain information for 1FLI.pdbqt #1
6435---
6436Chain | Description
6437A | No description available
6438
6439Opened 1FLI.pdbqt containing 1 structures (1589 atoms, 1612 bonds)
6440
6441> wait 5
6442
6443> hide surfaces
6444
6445> hide atoms
6446
6447> show cartoons
6448
6449> wait 5
6450
6451> addh
6452
6453Summary of feedback from adding hydrogens to 1FLI.pdbqt #1
6454---
6455notes | No usable SEQRES records for 1FLI.pdbqt (#1) chain A; guessing termini
6456instead
6457Chain-initial residues that are actual N termini: /A PRO 276
6458Chain-initial residues that are not actual N termini:
6459Chain-final residues that are actual C termini: /A PRO 373
6460Chain-final residues that are not actual C termini:
646138 hydrogen bonds
64621 hydrogens added
6463
6464
6465> wait 5
6466
6467> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1FLI--
6468> WRM-16.result.pdbqt
6469
6470Summary of feedback from opening
6471/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1FLI--WRM-16.result.pdbqt
6472---
6473warnings | Ignored bad PDB record found on line 2
6474REMARK VINA RESULT: -7.4 0.000 0.000
6475
6476Ignored bad PDB record found on line 3
6477REMARK 5 active torsions:
6478
6479Ignored bad PDB record found on line 4
6480REMARK status: ('A' for Active; 'I' for Inactive)
6481
6482Ignored bad PDB record found on line 5
6483REMARK 1 A between atoms: C_9 and O_15
6484
6485Ignored bad PDB record found on line 6
6486REMARK 2 A between atoms: C_10 and O_17
6487
6488184 messages similar to the above omitted
6489
6490Opened 1FLI--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
6491bonds)
6492
6493> wait 5
6494
6495> close #2.2-9
6496
6497> wait 5
6498
6499> contacts :UNL radius 0.05 log true saveFile
6500> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
6501> WRM-16.contacts.txt
6502
6503
6504 Allowed overlap: -0.4
6505 H-bond overlap reduction: 0.4
6506 Ignore contacts between atoms separated by 4 bonds or less
6507 Detect intra-residue contacts: False
6508 Detect intra-molecule contacts: True
6509
6510 45 contacts
6511 atom1 atom2 overlap distance
6512 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PHE 309 HE1 0.444 2.316
6513 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 1HD2 0.247 2.513
6514 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 1HD2 0.080 2.680
6515 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PHE 309 CE1 0.065 3.395
6516 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB3 0.055 2.555
6517 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ3 0.017 3.563
6518 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB3 0.004 2.606
6519 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PRO 371 HA -0.026 2.786
6520 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1FLI.pdbqt #1/A TRP 302 CD1 -0.029 3.609
6521 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 HZ3 -0.038 2.918
6522 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CB -0.055 3.515
6523 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PRO 371 CA -0.065 3.525
6524 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1FLI.pdbqt #1/A TRP 302 CG -0.089 3.669
6525 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 CD2 -0.091 3.551
6526 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 O -0.144 3.384
6527 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 2HD1 -0.165 2.925
6528 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CB -0.166 3.476
6529 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB3 -0.197 2.957
6530 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 CD2 -0.206 3.666
6531 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CH2 -0.224 3.684
6532 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ3 -0.228 3.688
6533 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 HH2 -0.228 2.838
6534 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PRO 371 N -0.247 3.632
6535 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CE2 -0.250 3.710
6536 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A TRP 302 HH2 -0.251 2.671
6537 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 C -0.269 3.729
6538 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A SER 292 CB -0.272 3.392
6539 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 3HD2 -0.277 2.887
6540 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CD2 -0.286 3.596
6541 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CD1 -0.287 3.747
6542 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 3HD2 -0.291 2.901
6543 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CB -0.294 3.604
6544 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CE3 -0.311 3.771
6545 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ2 -0.324 3.784
6546 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CE3 -0.330 3.790
6547 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 2HD1 -0.331 3.091
6548 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PHE 309 HE1 -0.348 3.108
6549 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CD1 -0.365 3.825
6550 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CD2 -0.368 3.828
6551 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB2 -0.373 3.133
6552 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ3 -0.388 3.698
6553 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A TRP 302 CH2 -0.390 3.550
6554 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A LEU 288 C -0.393 3.553
6555 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1FLI.pdbqt #1/A TRP 302 NE1 -0.396 3.901
6556 1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A GLN 370 C -0.400 3.860
6557
6558
6559
656045 contacts
6561
6562> hbonds :UNL showDist true radius 0.05 log true saveFile
6563> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
6564> WRM-16.hbonds.txt
6565
6566
6567 Finding intermodel H-bonds
6568 Finding intramodel H-bonds
6569 Constraints relaxed by 0.4 angstroms and 20 degrees
6570 Models used:
6571 1 1FLI.pdbqt
6572 2.1 1FLI--WRM-16.result.pdbqt
6573
6574 0 H-bonds
6575 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6576
6577
6578
65790 hydrogen bonds found
6580
6581> select :UNL
6582
658328 atoms, 31 bonds, 1 residue, 1 model selected
6584
6585> label sel text "Ligand "
6586
6587> label height 1
6588
6589> ~select
6590
6591Nothing selected
6592
6593> 2dlabels text "Binding Energy: -7.4 kcal/mol" color red size 18 xpos .03
6594> ypos .95
6595
6596> 2dlabels text "1FLI WRM-16 Complex" color gray size 18 xpos .03 ypos .91
6597
6598> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
6599> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
6600> true
6601
6602> select :UNL
6603
660428 atoms, 31 bonds, 1 residue, 1 model selected
6605
6606> view sel
6607
6608> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
6609> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
6610> true
6611
6612> close
6613
6614> wait 5
6615
6616> set bgColor white
6617
6618> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5LTY.pdbqt
6619
6620Chain information for 5LTY.pdbqt #1
6621---
6622Chain | Description
6623A B | No description available
6624E F | No description available
6625K | No description available
6626M | No description available
6627
6628Opened 5LTY.pdbqt containing 1 structures (4847 atoms, 5029 bonds)
6629
6630> wait 5
6631
6632> hide surfaces
6633
6634> hide atoms
6635
6636> show cartoons
6637
6638> wait 5
6639
6640> addh
6641
6642Summary of feedback from adding hydrogens to 5LTY.pdbqt #1
6643---
6644warnings | Not adding hydrogens to /A DT 1 P because it is missing heavy-atom
6645bond partners
6646Not adding hydrogens to /B DT 1 P because it is missing heavy-atom bond
6647partners
6648Not adding hydrogens to /F DG 19 P because it is missing heavy-atom bond
6649partners
6650Not adding hydrogens to /E DG 19 P because it is missing heavy-atom bond
6651partners
6652notes | No usable SEQRES records for 5LTY.pdbqt (#1) chain A; guessing termini
6653instead
6654No usable SEQRES records for 5LTY.pdbqt (#1) chain B; guessing termini instead
6655No usable SEQRES records for 5LTY.pdbqt (#1) chain E; guessing termini instead
6656No usable SEQRES records for 5LTY.pdbqt (#1) chain F; guessing termini instead
6657No usable SEQRES records for 5LTY.pdbqt (#1) chain K; guessing termini instead
66581 messages similar to the above omitted
6659Chain-initial residues that are actual N termini: /A DT 1, /B DT 1, /E DG 19,
6660/F DG 19, /K THR 185, /M LYS 186
6661Chain-initial residues that are not actual N termini: /A DG 12, /B DG 12, /E
6662DG 26, /F DG 26
6663Chain-final residues that are actual C termini: /A DC 18, /B DC 18, /E DA 36,
6664/F DA 36, /K GLN 255, /M GLN 255
6665Chain-final residues that are not actual C termini: /A DA 10, /B DA 10, /E DT
666624, /F DT 24
6667250 hydrogen bonds
66684 hydrogens added
6669
6670
6671> wait 5
6672
6673> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5LTY--
6674> WRM-16.result.pdbqt
6675
6676Summary of feedback from opening
6677/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5LTY--WRM-16.result.pdbqt
6678---
6679warnings | Ignored bad PDB record found on line 2
6680REMARK VINA RESULT: -8.4 0.000 0.000
6681
6682Ignored bad PDB record found on line 3
6683REMARK 5 active torsions:
6684
6685Ignored bad PDB record found on line 4
6686REMARK status: ('A' for Active; 'I' for Inactive)
6687
6688Ignored bad PDB record found on line 5
6689REMARK 1 A between atoms: C_9 and O_15
6690
6691Ignored bad PDB record found on line 6
6692REMARK 2 A between atoms: C_10 and O_17
6693
6694184 messages similar to the above omitted
6695
6696Opened 5LTY--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
6697bonds)
6698
6699> wait 5
6700
6701> close #2.2-9
6702
6703> wait 5
6704
6705> contacts :UNL radius 0.05 log true saveFile
6706> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
6707> WRM-16.contacts.txt
6708
6709
6710 Allowed overlap: -0.4
6711 H-bond overlap reduction: 0.4
6712 Ignore contacts between atoms separated by 4 bonds or less
6713 Detect intra-residue contacts: False
6714 Detect intra-molecule contacts: True
6715
6716 53 contacts
6717 atom1 atom2 overlap distance
6718 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 243 HZ2 0.418 2.462
6719 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 H73 0.241 2.639
6720 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 HB1 0.235 2.645
6721 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 243 NZ 0.227 3.278
6722 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H61 0.212 1.808
6723 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 HB2 0.183 2.577
6724 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 HB1 0.168 2.592
6725 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 9 H71 0.135 2.625
6726 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H71 0.114 2.766
6727 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H72 0.090 2.670
6728 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 28 H61 0.080 2.530
6729 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 CB 0.033 3.427
6730 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H71 0.003 2.877
6731 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 29 H61 -0.009 2.889
6732 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 C7 -0.033 3.613
6733 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DT 27 H73 -0.045 2.505
6734 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H72 -0.046 2.806
6735 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H72 -0.051 2.931
6736 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 CB -0.069 3.529
6737 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 CB -0.072 3.652
6738 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 OP2 -0.079 3.459
6739 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 9 C7 -0.099 3.559
6740 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 H73 -0.100 2.710
6741 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 H73 -0.122 3.002
6742 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 HB2 -0.125 2.735
6743 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H72 -0.130 2.740
6744 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H72 -0.133 2.743
6745 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M LYS 240 HB2 -0.145 3.025
6746 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.147 3.727
6747 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 O4 -0.148 3.508
6748 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 29 N6 -0.149 3.654
6749 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.153 3.613
6750 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 N6 -0.168 2.813
6751 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 C7 -0.179 3.489
6752 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 28 N6 -0.183 3.418
6753 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 C7 -0.193 3.503
6754 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/B DT 9 C7 -0.198 3.778
6755 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.209 3.669
6756 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 C -0.248 3.828
6757 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 CG -0.262 3.722
6758 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 C7 -0.285 3.595
6759 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H71 -0.289 2.899
6760 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M LYS 240 HD2 -0.299 3.179
6761 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H72 -0.302 2.912
6762 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H71 -0.305 3.185
6763 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 C7 -0.311 3.891
6764 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 O -0.320 3.560
6765 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DT 27 C5 -0.325 3.445
6766 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.349 3.929
6767 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 243 HZ3 -0.354 3.234
6768 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 O -0.369 3.729
6769 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DT 27 C7 -0.383 3.543
6770 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 HB1 -0.396 3.006
6771
6772
6773
677453 contacts
6775
6776> hbonds :UNL showDist true radius 0.05 log true saveFile
6777> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
6778> WRM-16.hbonds.txt
6779
6780
6781 Finding intermodel H-bonds
6782 Finding intramodel H-bonds
6783 Constraints relaxed by 0.4 angstroms and 20 degrees
6784 Models used:
6785 1 5LTY.pdbqt
6786 2.1 5LTY--WRM-16.result.pdbqt
6787
6788 3 H-bonds
6789 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6790 5LTY.pdbqt #1/E DA 28 N6 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H61 3.435 2.808
6791 5LTY.pdbqt #1/E DA 28 N6 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H61 2.813 1.808
6792 5LTY.pdbqt #1/E DA 28 N7 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H7 3.287 2.424
6793
6794
6795
67963 hydrogen bonds found
6797
6798> select :UNL
6799
680028 atoms, 31 bonds, 1 residue, 1 model selected
6801
6802> label sel text "Ligand "
6803
6804> label height 1
6805
6806> ~select
6807
6808Nothing selected
6809
6810> 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03
6811> ypos .95
6812
6813> 2dlabels text "5LTY WRM-16 Complex" color gray size 18 xpos .03 ypos .91
6814
6815> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
6816> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
6817> true
6818
6819> select :UNL
6820
682128 atoms, 31 bonds, 1 residue, 1 model selected
6822
6823> view sel
6824
6825> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
6826> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
6827> true
6828
6829> close
6830
6831> wait 5
6832
6833> set bgColor white
6834
6835> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1JDH.pdbqt
6836
6837Chain information for 1JDH.pdbqt #1
6838---
6839Chain | Description
6840A | No description available
6841B | No description available
6842
6843Opened 1JDH.pdbqt containing 1 structures (8191 atoms, 8243 bonds)
6844
6845> wait 5
6846
6847> hide surfaces
6848
6849> hide atoms
6850
6851> show cartoons
6852
6853> wait 5
6854
6855> addh
6856
6857Summary of feedback from adding hydrogens to 1JDH.pdbqt #1
6858---
6859warnings | Not adding hydrogens to /A ILE 140 CB because it is missing heavy-
6860atom bond partners
6861Not adding hydrogens to /A ARG 151 CB because it is missing heavy-atom bond
6862partners
6863Not adding hydrogens to /A LYS 158 CB because it is missing heavy-atom bond
6864partners
6865Not adding hydrogens to /A GLU 163 CB because it is missing heavy-atom bond
6866partners
6867Not adding hydrogens to /A GLN 177 CB because it is missing heavy-atom bond
6868partners
686928 messages similar to the above omitted
6870notes | No usable SEQRES records for 1JDH.pdbqt (#1) chain A; guessing termini
6871instead
6872No usable SEQRES records for 1JDH.pdbqt (#1) chain B; guessing termini instead
6873Chain-initial residues that are actual N termini: /A ALA 135, /B LEU 12
6874Chain-initial residues that are not actual N termini: /A ARG 151, /A PHE 560
6875Chain-final residues that are actual C termini: /A SER 663, /B VAL 49
6876Chain-final residues that are not actual C termini: /A ILE 140, /A GLN 548
6877502 hydrogen bonds
6878Adding 'H' to /A ARG 151
6879Adding 'H' to /A PHE 560
6880/A ILE 140 is not terminus, removing H atom from 'C'
6881/A GLN 548 is not terminus, removing H atom from 'C'
68825 hydrogens added
6883
6884
6885> wait 5
6886
6887> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1JDH--
6888> WRM-16.result.pdbqt
6889
6890Summary of feedback from opening
6891/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1JDH--WRM-16.result.pdbqt
6892---
6893warnings | Ignored bad PDB record found on line 2
6894REMARK VINA RESULT: -6.7 0.000 0.000
6895
6896Ignored bad PDB record found on line 3
6897REMARK 5 active torsions:
6898
6899Ignored bad PDB record found on line 4
6900REMARK status: ('A' for Active; 'I' for Inactive)
6901
6902Ignored bad PDB record found on line 5
6903REMARK 1 A between atoms: C_9 and O_15
6904
6905Ignored bad PDB record found on line 6
6906REMARK 2 A between atoms: C_10 and O_17
6907
6908184 messages similar to the above omitted
6909
6910Opened 1JDH--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
6911bonds)
6912
6913> wait 5
6914
6915> close #2.2-9
6916
6917> wait 5
6918
6919> contacts :UNL radius 0.05 log true saveFile
6920> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
6921> WRM-16.contacts.txt
6922
6923
6924 Allowed overlap: -0.4
6925 H-bond overlap reduction: 0.4
6926 Ignore contacts between atoms separated by 4 bonds or less
6927 Detect intra-residue contacts: False
6928 Detect intra-molecule contacts: True
6929
6930 49 contacts
6931 atom1 atom2 overlap distance
6932 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 2HG1 0.358 2.522
6933 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HE 0.338 2.542
6934 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 HE 0.255 1.805
6935 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLU 163 HA 0.243 2.517
6936 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 HA 0.123 2.757
6937 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 HB2 0.103 2.357
6938 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 3HG2 0.097 2.783
6939 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HB2 0.055 2.555
6940 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 CG1 0.046 3.534
6941 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 CA 0.013 3.567
6942 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 NE 0.003 3.502
6943 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 CB -0.018 3.598
6944 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A THR 201 HA -0.027 2.487
6945 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 CB -0.038 3.198
6946 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 2HH2 -0.088 2.968
6947 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 HB1 -0.090 2.850
6948 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 ND2 -0.106 3.611
6949 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLN 165 1HE2 -0.115 2.995
6950 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 NE -0.118 2.803
6951 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ASN 161 HA -0.118 2.538
6952 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 1HD2 -0.126 2.736
6953 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 CG2 -0.146 3.726
6954 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HB2 -0.155 3.035
6955 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLU 163 CA -0.159 3.619
6956 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLU 163 HA -0.171 2.781
6957 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 CB -0.177 3.487
6958 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 CB -0.204 3.664
6959 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 HB2 -0.206 3.086
6960 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 1HD2 -0.213 2.823
6961 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A THR 201 OG1 -0.218 2.738
6962 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASP 162 O -0.235 3.475
6963 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 CB -0.251 3.561
6964 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 NH2 -0.267 3.772
6965 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ASN 161 CA -0.284 3.404
6966 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLN 165 OE1 -0.287 3.647
6967 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HE -0.295 3.175
6968 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 161 O -0.303 3.543
6969 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 ND2 -0.310 3.545
6970 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 CZ -0.336 3.496
6971 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 HB1 -0.340 2.950
6972 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HE -0.356 2.966
6973 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 O -0.363 3.723
6974 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A LEU 160 O -0.365 3.725
6975 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 HB1 -0.368 3.128
6976 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 ND2 -0.369 3.604
6977 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A THR 201 2HG2 -0.380 3.260
6978 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A THR 201 CA -0.385 3.545
6979 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 CB -0.389 3.969
6980 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 2HH2 -0.395 2.415
6981
6982
6983
698449 contacts
6985
6986> hbonds :UNL showDist true radius 0.05 log true saveFile
6987> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
6988> WRM-16.hbonds.txt
6989
6990
6991 Finding intermodel H-bonds
6992 Finding intramodel H-bonds
6993 Constraints relaxed by 0.4 angstroms and 20 degrees
6994 Models used:
6995 1 1JDH.pdbqt
6996 2.1 1JDH--WRM-16.result.pdbqt
6997
6998 4 H-bonds
6999 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
7000 1JDH.pdbqt #1/A ASN 161 ND2 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ASN 161 1HD2 3.118 2.516
7001 1JDH.pdbqt #1/A ARG 200 NE 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 HE 2.803 1.805
7002 1JDH.pdbqt #1/A ARG 200 NH2 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 2HH2 3.325 2.546
7003 1JDH.pdbqt #1/A ARG 200 NH2 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 2HH2 3.343 2.415
7004
7005
7006
70074 hydrogen bonds found
7008
7009> select :UNL
7010
701128 atoms, 31 bonds, 1 residue, 1 model selected
7012
7013> label sel text "Ligand "
7014
7015> label height 1
7016
7017> ~select
7018
7019Nothing selected
7020
7021> 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
7022> ypos .95
7023
7024> 2dlabels text "1JDH WRM-16 Complex" color gray size 18 xpos .03 ypos .91
7025
7026> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
7027> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
7028> true
7029
7030> select :UNL
7031
703228 atoms, 31 bonds, 1 residue, 1 model selected
7033
7034> view sel
7035
7036> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
7037> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
7038> true
7039
7040> close
7041
7042> wait 5
7043
7044> set bgColor white
7045
7046> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/6LZP.pdbqt
7047
7048Chain information for 6LZP.pdbqt #1
7049---
7050Chain | Description
7051A | No description available
7052
7053Opened 6LZP.pdbqt containing 1 structures (1381 atoms, 1395 bonds)
7054
7055> wait 5
7056
7057> hide surfaces
7058
7059> hide atoms
7060
7061> show cartoons
7062
7063> wait 5
7064
7065> addh
7066
7067Summary of feedback from adding hydrogens to 6LZP.pdbqt #1
7068---
7069notes | No usable SEQRES records for 6LZP.pdbqt (#1) chain A; guessing termini
7070instead
7071Chain-initial residues that are actual N termini: /A HIS 171
7072Chain-initial residues that are not actual N termini:
7073Chain-final residues that are actual C termini: /A SER 258
7074Chain-final residues that are not actual C termini:
707535 hydrogen bonds
70761 hydrogens added
7077
7078
7079> wait 5
7080
7081> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LZP--
7082> WRM-16.result.pdbqt
7083
7084Summary of feedback from opening
7085/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LZP--WRM-16.result.pdbqt
7086---
7087warnings | Ignored bad PDB record found on line 2
7088REMARK VINA RESULT: -6.5 0.000 0.000
7089
7090Ignored bad PDB record found on line 3
7091REMARK 5 active torsions:
7092
7093Ignored bad PDB record found on line 4
7094REMARK status: ('A' for Active; 'I' for Inactive)
7095
7096Ignored bad PDB record found on line 5
7097REMARK 1 A between atoms: C_9 and O_15
7098
7099Ignored bad PDB record found on line 6
7100REMARK 2 A between atoms: C_10 and O_17
7101
7102184 messages similar to the above omitted
7103
7104Opened 6LZP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
7105bonds)
7106
7107> wait 5
7108
7109> close #2.2-9
7110
7111> wait 5
7112
7113> contacts :UNL radius 0.05 log true saveFile
7114> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
7115> WRM-16.contacts.txt
7116
7117
7118 Allowed overlap: -0.4
7119 H-bond overlap reduction: 0.4
7120 Ignore contacts between atoms separated by 4 bonds or less
7121 Detect intra-residue contacts: False
7122 Detect intra-molecule contacts: True
7123
7124 42 contacts
7125 atom1 atom2 overlap distance
7126 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 HE3 0.364 2.516
7127 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HG2 0.319 2.441
7128 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PHE 204 HE1 0.260 2.620
7129 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 CE3 0.181 3.399
7130 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 HA 0.168 2.712
7131 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 0.150 2.460
7132 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 CA 0.145 3.435
7133 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PHE 204 CE1 0.125 3.455
7134 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 N 0.050 3.455
7135 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HE1 0.040 2.840
7136 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 H 0.034 1.986
7137 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 H -0.009 2.619
7138 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 HE1 -0.027 2.637
7139 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 CG -0.029 3.489
7140 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A THR 214 C -0.067 3.647
7141 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 HG1 -0.077 2.687
7142 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 HB2 -0.091 2.701
7143 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HG2 -0.093 2.703
7144 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HB2 -0.114 2.874
7145 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 -0.120 2.880
7146 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 CZ3 -0.132 3.712
7147 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 HG1 -0.139 2.159
7148 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HG2 -0.146 2.906
7149 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CE2 -0.174 3.484
7150 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 O -0.176 3.116
7151 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 -0.179 2.789
7152 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 HE1 -0.191 2.951
7153 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 CE -0.193 3.773
7154 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 CE1 -0.195 3.505
7155 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 -0.234 2.844
7156 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 CB -0.256 3.836
7157 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CE2 -0.256 3.566
7158 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 N -0.271 3.506
7159 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A TRP 206 HE3 -0.271 3.031
7160 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CB -0.294 3.754
7161 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 CG -0.298 3.758
7162 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 CB -0.314 3.894
7163 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 N -0.320 2.965
7164 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 HZ3 -0.324 3.204
7165 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PHE 204 CZ -0.337 3.917
7166 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 OG1 -0.354 3.464
7167 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CE2 -0.361 3.821
7168
7169
7170
717142 contacts
7172
7173> hbonds :UNL showDist true radius 0.05 log true saveFile
7174> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
7175> WRM-16.hbonds.txt
7176
7177
7178 Finding intermodel H-bonds
7179 Finding intramodel H-bonds
7180 Constraints relaxed by 0.4 angstroms and 20 degrees
7181 Models used:
7182 1 6LZP.pdbqt
7183 2.1 6LZP--WRM-16.result.pdbqt
7184
7185 2 H-bonds
7186 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
7187 6LZP.pdbqt #1/A THR 205 N 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 H 2.965 1.986
7188 6LZP.pdbqt #1/A THR 205 OG1 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 HG1 3.071 2.159
7189
7190
7191
71922 hydrogen bonds found
7193
7194> select :UNL
7195
719628 atoms, 31 bonds, 1 residue, 1 model selected
7197
7198> label sel text "Ligand "
7199
7200> label height 1
7201
7202> ~select
7203
7204Nothing selected
7205
7206> 2dlabels text "Binding Energy: -6.5 kcal/mol" color red size 18 xpos .03
7207> ypos .95
7208
7209> 2dlabels text "6LZP WRM-16 Complex" color gray size 18 xpos .03 ypos .91
7210
7211> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
7212> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
7213> true
7214
7215> select :UNL
7216
721728 atoms, 31 bonds, 1 residue, 1 model selected
7218
7219> view sel
7220
7221> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
7222> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
7223> true
7224
7225> close
7226
7227> wait 5
7228
7229> set bgColor white
7230
7231> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2CS1.pdbqt
7232
7233Chain information for 2CS1.pdbqt #1
7234---
7235Chain | Description
7236A | No description available
7237
7238Opened 2CS1.pdbqt containing 1 structures (1441 atoms, 1451 bonds)
7239
7240> wait 5
7241
7242> hide surfaces
7243
7244> hide atoms
7245
7246> show cartoons
7247
7248> wait 5
7249
7250> addh
7251
7252Summary of feedback from adding hydrogens to 2CS1.pdbqt #1
7253---
7254notes | No usable SEQRES records for 2CS1.pdbqt (#1) chain A; guessing termini
7255instead
7256Chain-initial residues that are actual N termini: /A GLY 1
7257Chain-initial residues that are not actual N termini:
7258Chain-final residues that are actual C termini: /A GLY 92
7259Chain-final residues that are not actual C termini:
726043 hydrogen bonds
72611 hydrogens added
7262
7263
7264> wait 5
7265
7266> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CS1--
7267> WRM-16.result.pdbqt
7268
7269Summary of feedback from opening
7270/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CS1--WRM-16.result.pdbqt
7271---
7272warnings | Ignored bad PDB record found on line 2
7273REMARK VINA RESULT: -7.0 0.000 0.000
7274
7275Ignored bad PDB record found on line 3
7276REMARK 5 active torsions:
7277
7278Ignored bad PDB record found on line 4
7279REMARK status: ('A' for Active; 'I' for Inactive)
7280
7281Ignored bad PDB record found on line 5
7282REMARK 1 A between atoms: C_9 and O_15
7283
7284Ignored bad PDB record found on line 6
7285REMARK 2 A between atoms: C_10 and O_17
7286
7287184 messages similar to the above omitted
7288
7289Opened 2CS1--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
7290bonds)
7291
7292> wait 5
7293
7294> close #2.2-9
7295
7296> wait 5
7297
7298> contacts :UNL radius 0.05 log true saveFile
7299> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
7300> WRM-16.contacts.txt
7301
7302
7303 Allowed overlap: -0.4
7304 H-bond overlap reduction: 0.4
7305 Ignore contacts between atoms separated by 4 bonds or less
7306 Detect intra-residue contacts: False
7307 Detect intra-molecule contacts: True
7308
7309 50 contacts
7310 atom1 atom2 overlap distance
7311 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 14 HB2 0.371 2.389
7312 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A SER 13 HG 0.226 1.834
7313 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 61 HB1 0.195 2.685
7314 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HD2 0.150 2.610
7315 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 HG2 0.131 2.629
7316 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HG2 0.080 2.680
7317 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 HD2 0.072 2.688
7318 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 14 CB 0.013 3.447
7319 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD1 -0.019 3.599
7320 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HG -0.028 2.908
7321 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 HG2 -0.041 2.801
7322 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 3HD1 -0.049 2.929
7323 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HG -0.068 2.948
7324 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 OG -0.074 3.454
7325 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TYR 68 CE2 -0.090 3.550
7326 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CG -0.104 3.564
7327 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CD -0.117 3.577
7328 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HG -0.124 2.734
7329 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CS1.pdbqt #1/A LYS 54 HZ1 -0.129 3.009
7330 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A SER 13 OG -0.138 2.698
7331 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 61 CB -0.158 3.738
7332 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 CG -0.166 3.626
7333 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 CD -0.172 3.632
7334 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CS1.pdbqt #1/A LYS 54 HD3 -0.195 3.075
7335 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLY 1 HN -0.208 2.968
7336 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 61 O -0.211 3.571
7337 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD1 -0.220 3.530
7338 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 OE1 -0.227 3.467
7339 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HG2 -0.229 3.109
7340 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TYR 68 CD2 -0.237 3.697
7341 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A ALA 61 HB3 -0.242 2.662
7342 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLY 1 HA2 -0.267 3.147
7343 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 CG -0.272 3.732
7344 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 OE1 -0.276 3.516
7345 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HA -0.296 3.176
7346 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HD2 -0.304 3.064
7347 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 2HD1 -0.327 2.937
7348 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CD -0.330 3.790
7349 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 HB3 -0.331 3.091
7350 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 CB -0.332 3.912
7351 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD1 -0.334 3.644
7352 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TYR 68 CZ -0.337 3.797
7353 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CS1.pdbqt #1/A LYS 54 NZ -0.359 3.864
7354 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 OG -0.373 3.483
7355 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 HD2 -0.378 3.138
7356 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLY 1 N -0.379 3.764
7357 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CG -0.380 3.840
7358 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TRP 46 HZ2 -0.386 3.146
7359 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A ALA 61 CB -0.386 3.506
7360 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD2 -0.388 3.968
7361
7362
7363
736450 contacts
7365
7366> hbonds :UNL showDist true radius 0.05 log true saveFile
7367> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
7368> WRM-16.hbonds.txt
7369
7370
7371 Finding intermodel H-bonds
7372 Finding intramodel H-bonds
7373 Constraints relaxed by 0.4 angstroms and 20 degrees
7374 Models used:
7375 1 2CS1.pdbqt
7376 2.1 2CS1--WRM-16.result.pdbqt
7377
7378 1 H-bonds
7379 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
7380 2CS1.pdbqt #1/A SER 13 OG 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A SER 13 HG 2.698 1.834
7381
7382
7383
73841 hydrogen bonds found
7385
7386> select :UNL
7387
738828 atoms, 31 bonds, 1 residue, 1 model selected
7389
7390> label sel text "Ligand "
7391
7392> label height 1
7393
7394> ~select
7395
7396Nothing selected
7397
7398> 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03
7399> ypos .95
7400
7401> 2dlabels text "2CS1 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
7402
7403> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
7404> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
7405> true
7406
7407> select :UNL
7408
740928 atoms, 31 bonds, 1 residue, 1 model selected
7410
7411> view sel
7412
7413> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
7414> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
7415> true
7416
7417> close
7418
7419> wait 5
7420
7421> set bgColor white
7422
7423> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2GU8.pdbqt
7424
7425Chain information for 2GU8.pdbqt #1
7426---
7427Chain | Description
7428A | No description available
7429C | No description available
7430
7431Opened 2GU8.pdbqt containing 1 structures (5803 atoms, 5874 bonds)
7432
7433> wait 5
7434
7435> hide surfaces
7436
7437> hide atoms
7438
7439> show cartoons
7440
7441> wait 5
7442
7443> addh
7444
7445Summary of feedback from adding hydrogens to 2GU8.pdbqt #1
7446---
7447warnings | Not adding hydrogens to /A VAL 15 CB because it is missing heavy-
7448atom bond partners
7449Not adding hydrogens to /A LYS 16 CB because it is missing heavy-atom bond
7450partners
7451Not adding hydrogens to /A GLU 17 CB because it is missing heavy-atom bond
7452partners
7453Not adding hydrogens to /A LYS 21 CB because it is missing heavy-atom bond
7454partners
7455notes | No usable SEQRES records for 2GU8.pdbqt (#1) chain A; guessing termini
7456instead
7457No usable SEQRES records for 2GU8.pdbqt (#1) chain C; guessing termini instead
7458Chain-initial residues that are actual N termini: /A SER 14, /C THR 505
7459Chain-initial residues that are not actual N termini: /A LEU 198, /A ILE 339
7460Chain-final residues that are actual C termini: /A PHE 350, /C ASP 524
7461Chain-final residues that are not actual C termini: /A TRP 196, /A VAL 337
7462290 hydrogen bonds
7463Adding 'H' to /A LEU 198
7464Adding 'H' to /A ILE 339
7465/A TRP 196 is not terminus, removing H atom from 'C'
7466/A VAL 337 is not terminus, removing H atom from 'C'
7467-2 hydrogens added
7468
7469
7470> wait 5
7471
7472> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2GU8--
7473> WRM-16.result.pdbqt
7474
7475Summary of feedback from opening
7476/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2GU8--WRM-16.result.pdbqt
7477---
7478warnings | Ignored bad PDB record found on line 2
7479REMARK VINA RESULT: -8.1 0.000 0.000
7480
7481Ignored bad PDB record found on line 3
7482REMARK 5 active torsions:
7483
7484Ignored bad PDB record found on line 4
7485REMARK status: ('A' for Active; 'I' for Inactive)
7486
7487Ignored bad PDB record found on line 5
7488REMARK 1 A between atoms: C_9 and O_15
7489
7490Ignored bad PDB record found on line 6
7491REMARK 2 A between atoms: C_10 and O_17
7492
7493184 messages similar to the above omitted
7494
7495Opened 2GU8--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
7496bonds)
7497
7498> wait 5
7499
7500> close #2.2-9
7501
7502> wait 5
7503
7504> contacts :UNL radius 0.05 log true saveFile
7505> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
7506> WRM-16.contacts.txt
7507
7508
7509 Allowed overlap: -0.4
7510 H-bond overlap reduction: 0.4
7511 Ignore contacts between atoms separated by 4 bonds or less
7512 Detect intra-residue contacts: False
7513 Detect intra-molecule contacts: True
7514
7515 57 contacts
7516 atom1 atom2 overlap distance
7517 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HG2 0.382 2.498
7518 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 O 0.347 3.013
7519 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 HN 0.332 2.428
7520 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 313 HD1 0.278 2.602
7521 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 HA 0.244 2.516
7522 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A VAL 310 3HG2 0.217 2.663
7523 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A VAL 310 CG2 0.191 3.269
7524 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 HB2 0.173 2.707
7525 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 HE 0.160 1.900
7526 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HE 0.104 2.506
7527 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A VAL 310 1HG2 0.094 2.666
7528 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 313 CD 0.077 3.503
7529 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A ASP 301 HB2 0.074 2.806
7530 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 HN 0.042 2.718
7531 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 HG1 0.035 1.985
7532 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 CG 0.002 3.578
7533 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 O -0.001 3.241
7534 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 N -0.038 3.423
7535 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 HA -0.045 2.655
7536 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CB -0.051 3.631
7537 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 1HH2 -0.078 2.098
7538 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A PRO 141 HA -0.089 2.549
7539 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A VAL 310 CG2 -0.106 3.686
7540 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A ASP 301 CB -0.132 3.712
7541 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 CA -0.133 3.593
7542 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 3HG2 -0.136 2.896
7543 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 1HH2 -0.140 2.750
7544 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 NE -0.171 2.856
7545 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A VAL 310 3HG2 -0.210 2.970
7546 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A GLU 311 O -0.241 3.601
7547 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 313 CG -0.249 3.829
7548 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CD1 -0.251 3.831
7549 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 CD -0.252 3.372
7550 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 C -0.252 3.832
7551 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 O -0.253 3.493
7552 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 NE -0.260 3.495
7553 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 N -0.268 3.653
7554 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 HB -0.289 3.169
7555 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HG2 -0.290 3.170
7556 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CG -0.293 3.873
7557 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A PRO 141 CA -0.296 3.456
7558 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A VAL 310 CG1 -0.301 3.461
7559 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HE -0.306 3.186
7560 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 CG2 -0.311 3.771
7561 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 300 CA -0.313 3.433
7562 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 HB2 -0.319 3.079
7563 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 N -0.333 3.838
7564 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 CA -0.337 3.917
7565 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CA -0.342 3.922
7566 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ILE 305 1HD1 -0.361 3.121
7567 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 C -0.363 3.483
7568 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 HB2 -0.372 2.982
7569 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 NH2 -0.373 3.018
7570 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 OG1 -0.378 2.898
7571 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 OG1 -0.384 3.494
7572 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 HG2 -0.393 2.813
7573 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 HA -0.395 3.275
7574
7575
7576
757757 contacts
7578
7579> hbonds :UNL showDist true radius 0.05 log true saveFile
7580> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
7581> WRM-16.hbonds.txt
7582
7583
7584 Finding intermodel H-bonds
7585 Finding intramodel H-bonds
7586 Constraints relaxed by 0.4 angstroms and 20 degrees
7587 Models used:
7588 1 2GU8.pdbqt
7589 2.1 2GU8--WRM-16.result.pdbqt
7590
7591 3 H-bonds
7592 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
7593 2GU8.pdbqt #1/A ARG 144 NE 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 HE 2.856 1.900
7594 2GU8.pdbqt #1/A ARG 144 NH2 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 1HH2 3.018 2.098
7595 2GU8.pdbqt #1/A THR 299 OG1 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 HG1 2.898 1.985
7596
7597
7598
75993 hydrogen bonds found
7600
7601> select :UNL
7602
760328 atoms, 31 bonds, 1 residue, 1 model selected
7604
7605> label sel text "Ligand "
7606
7607> label height 1
7608
7609> ~select
7610
7611Nothing selected
7612
7613> 2dlabels text "Binding Energy: -8.1 kcal/mol" color red size 18 xpos .03
7614> ypos .95
7615
7616> 2dlabels text "2GU8 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
7617
7618> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
7619> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
7620> true
7621
7622> select :UNL
7623
762428 atoms, 31 bonds, 1 residue, 1 model selected
7625
7626> view sel
7627
7628> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
7629> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
7630> true
7631
7632> close
7633
7634> wait 5
7635
7636> set bgColor white
7637
7638> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5VTB.pdbqt
7639
7640Chain information for 5VTB.pdbqt #1
7641---
7642Chain | Description
7643A | No description available
7644B | No description available
7645
7646Opened 5VTB.pdbqt containing 1 structures (5433 atoms, 5510 bonds)
7647
7648> wait 5
7649
7650> hide surfaces
7651
7652> hide atoms
7653
7654> show cartoons
7655
7656> wait 5
7657
7658> addh
7659
7660Summary of feedback from adding hydrogens to 5VTB.pdbqt #1
7661---
7662warnings | Not adding hydrogens to /A LYS 25 CB because it is missing heavy-
7663atom bond partners
7664Not adding hydrogens to /A LYS 26 CB because it is missing heavy-atom bond
7665partners
7666Not adding hydrogens to /A VAL 35 CB because it is missing heavy-atom bond
7667partners
7668Not adding hydrogens to /A ASP 52 CB because it is missing heavy-atom bond
7669partners
7670Not adding hydrogens to /A LYS 59 CB because it is missing heavy-atom bond
7671partners
767232 messages similar to the above omitted
7673notes | No usable SEQRES records for 5VTB.pdbqt (#1) chain A; guessing termini
7674instead
7675No usable SEQRES records for 5VTB.pdbqt (#1) chain B; guessing termini instead
7676Chain-initial residues that are actual N termini: /A LYS 25, /B ARG 3
7677Chain-initial residues that are not actual N termini: /A LYS 59, /A GLY 113,
7678/A PRO 363
7679Chain-final residues that are actual C termini: /A ASP 411, /B GLU 16
7680Chain-final residues that are not actual C termini: /A THR 54, /A ASN 88, /A
7681GLU 352
7682287 hydrogen bonds
7683Adding 'H' to /A LYS 59
7684Adding 'H' to /A GLY 113
7685/A THR 54 is not terminus, removing H atom from 'C'
7686/A ASN 88 is not terminus, removing H atom from 'C'
7687/A GLU 352 is not terminus, removing H atom from 'C'
7688-2 hydrogens added
7689
7690
7691> wait 5
7692
7693> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VTB--
7694> WRM-16.result.pdbqt
7695
7696Summary of feedback from opening
7697/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VTB--WRM-16.result.pdbqt
7698---
7699warnings | Ignored bad PDB record found on line 2
7700REMARK VINA RESULT: -8.4 0.000 0.000
7701
7702Ignored bad PDB record found on line 3
7703REMARK 5 active torsions:
7704
7705Ignored bad PDB record found on line 4
7706REMARK status: ('A' for Active; 'I' for Inactive)
7707
7708Ignored bad PDB record found on line 5
7709REMARK 1 A between atoms: C_9 and O_15
7710
7711Ignored bad PDB record found on line 6
7712REMARK 2 A between atoms: C_10 and O_17
7713
7714184 messages similar to the above omitted
7715
7716Opened 5VTB--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
7717bonds)
7718
7719> wait 5
7720
7721> close #2.2-9
7722
7723> wait 5
7724
7725> contacts :UNL radius 0.05 log true saveFile
7726> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
7727> WRM-16.contacts.txt
7728
7729
7730 Allowed overlap: -0.4
7731 H-bond overlap reduction: 0.4
7732 Ignore contacts between atoms separated by 4 bonds or less
7733 Detect intra-residue contacts: False
7734 Detect intra-molecule contacts: True
7735
7736 47 contacts
7737 atom1 atom2 overlap distance
7738 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 2HE2 0.542 2.338
7739 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 HB2 0.411 2.469
7740 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 NE2 0.359 3.146
7741 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A TRP 382 O 0.261 3.099
7742 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 185 HN 0.260 2.500
7743 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CB 0.243 3.337
7744 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 HB2 0.217 2.543
7745 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 HG1 0.111 2.769
7746 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 HA 0.106 2.654
7747 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 HB2 0.056 2.554
7748 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 HG -0.008 2.028
7749 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CA -0.067 3.647
7750 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 280 HA -0.085 2.505
7751 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 CG -0.089 3.669
7752 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A TRP 325 HB1 -0.103 2.523
7753 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 2HE2 -0.108 2.988
7754 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 185 N -0.114 3.499
7755 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 2HE2 -0.124 2.734
7756 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 OG -0.150 3.410
7757 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 234 HG -0.157 2.767
7758 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 HB2 -0.165 3.045
7759 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 CB -0.167 3.747
7760 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 382 HB2 -0.167 2.927
7761 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 CA -0.177 3.637
7762 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 HA -0.183 2.943
7763 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 CB -0.192 3.652
7764 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 CB -0.197 3.507
7765 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A LEU 183 O -0.205 3.565
7766 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 N -0.232 3.737
7767 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 OG -0.239 2.759
7768 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CD -0.256 3.836
7769 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 325 O -0.266 3.506
7770 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 1HE2 -0.291 3.051
7771 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 185 HN -0.309 3.069
7772 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A GLN 324 OE1 -0.311 3.251
7773 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A VAL 233 O -0.314 3.674
7774 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 CD -0.319 3.899
7775 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 234 OG -0.319 3.429
7776 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 OG -0.328 2.888
7777 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 NE2 -0.330 3.715
7778 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 HA -0.334 3.214
7779 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 CB -0.341 3.461
7780 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 NE2 -0.343 3.728
7781 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 CB -0.350 3.510
7782 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A LEU 279 O -0.370 3.270
7783 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 1HE2 -0.379 3.139
7784 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CG -0.388 3.968
7785
7786
7787
778847 contacts
7789
7790> hbonds :UNL showDist true radius 0.05 log true saveFile
7791> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
7792> WRM-16.hbonds.txt
7793
7794
7795 Finding intermodel H-bonds
7796 Finding intramodel H-bonds
7797 Constraints relaxed by 0.4 angstroms and 20 degrees
7798 Models used:
7799 1 5VTB.pdbqt
7800 2.1 5VTB--WRM-16.result.pdbqt
7801
7802 1 H-bonds
7803 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
7804 5VTB.pdbqt #1/A SER 234 OG 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 HG 2.759 2.028
7805
7806
7807
78081 hydrogen bonds found
7809
7810> select :UNL
7811
781228 atoms, 31 bonds, 1 residue, 1 model selected
7813
7814> label sel text "Ligand "
7815
7816> label height 1
7817
7818> ~select
7819
7820Nothing selected
7821
7822> 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03
7823> ypos .95
7824
7825> 2dlabels text "5VTB WRM-16 Complex" color gray size 18 xpos .03 ypos .91
7826
7827> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
7828> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
7829> true
7830
7831> select :UNL
7832
783328 atoms, 31 bonds, 1 residue, 1 model selected
7834
7835> view sel
7836
7837> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
7838> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
7839> true
7840
7841> close
7842
7843> wait 5
7844
7845> set bgColor white
7846
7847> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2D3J.pdbqt
7848
7849Chain information for 2D3J.pdbqt #1
7850---
7851Chain | Description
7852A | No description available
7853
7854Opened 2D3J.pdbqt containing 1 structures (2441 atoms, 2470 bonds)
7855
7856> wait 5
7857
7858> hide surfaces
7859
7860> hide atoms
7861
7862> show cartoons
7863
7864> wait 5
7865
7866> addh
7867
7868Summary of feedback from adding hydrogens to 2D3J.pdbqt #1
7869---
7870notes | No usable SEQRES records for 2D3J.pdbqt (#1) chain A; guessing termini
7871instead
7872Chain-initial residues that are actual N termini: /A GLY 1
7873Chain-initial residues that are not actual N termini:
7874Chain-final residues that are actual C termini: /A GLU 157
7875Chain-final residues that are not actual C termini:
7876134 hydrogen bonds
78772 hydrogens added
7878
7879
7880> wait 5
7881
7882> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D3J--
7883> WRM-16.result.pdbqt
7884
7885Summary of feedback from opening
7886/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D3J--WRM-16.result.pdbqt
7887---
7888warnings | Ignored bad PDB record found on line 2
7889REMARK VINA RESULT: -6.9 0.000 0.000
7890
7891Ignored bad PDB record found on line 3
7892REMARK 5 active torsions:
7893
7894Ignored bad PDB record found on line 4
7895REMARK status: ('A' for Active; 'I' for Inactive)
7896
7897Ignored bad PDB record found on line 5
7898REMARK 1 A between atoms: C_9 and O_15
7899
7900Ignored bad PDB record found on line 6
7901REMARK 2 A between atoms: C_10 and O_17
7902
7903184 messages similar to the above omitted
7904
7905Opened 2D3J--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
7906bonds)
7907
7908> wait 5
7909
7910> close #2.2-9
7911
7912> wait 5
7913
7914> contacts :UNL radius 0.05 log true saveFile
7915> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
7916> WRM-16.contacts.txt
7917
7918
7919 Allowed overlap: -0.4
7920 H-bond overlap reduction: 0.4
7921 Ignore contacts between atoms separated by 4 bonds or less
7922 Detect intra-residue contacts: False
7923 Detect intra-molecule contacts: True
7924
7925 45 contacts
7926 atom1 atom2 overlap distance
7927 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D3J.pdbqt #1/A LEU 85 2HD1 0.384 2.496
7928 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 55 HB3 0.246 2.514
7929 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ 0.218 2.542
7930 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D3J.pdbqt #1/A LEU 85 CD1 0.198 3.382
7931 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A VAL 123 3HG1 0.151 2.609
7932 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 N 0.137 3.368
7933 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CZ 0.129 3.451
7934 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 3HD1 0.115 2.645
7935 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 3HG2 0.068 2.692
7936 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 HB3 0.051 2.829
7937 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 HD3 -0.008 2.888
7938 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 55 CB -0.044 3.504
7939 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 HD3 -0.047 2.657
7940 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 HD3 -0.064 2.824
7941 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 CA -0.071 3.651
7942 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CD2 -0.087 3.667
7943 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ -0.097 2.977
7944 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 CB -0.100 3.680
7945 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CE2 -0.125 3.705
7946 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 CD -0.137 3.717
7947 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ -0.142 2.752
7948 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CZ -0.164 3.624
7949 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 CD1 -0.196 3.656
7950 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CB -0.221 3.681
7951 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A VAL 123 CG1 -0.221 3.681
7952 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A VAL 123 3HG1 -0.232 2.992
7953 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CG -0.235 3.695
7954 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PRO 54 HB2 -0.236 2.996
7955 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CD2 -0.247 3.557
7956 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A LYS 48 C -0.250 3.830
7957 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 3HG2 -0.280 3.040
7958 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 CG2 -0.287 3.747
7959 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HD2 -0.289 3.169
7960 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CD1 -0.292 3.752
7961 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CE1 -0.296 3.876
7962 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D3J.pdbqt #1/A ARG 47 NH1 -0.304 2.949
7963 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ -0.325 3.085
7964 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D3J.pdbqt #1/A ARG 47 1HH1 -0.329 2.349
7965 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 CD -0.348 3.658
7966 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CG -0.349 3.659
7967 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CB -0.352 3.812
7968 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HE2 -0.357 3.237
7969 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 CD -0.365 3.825
7970 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 O -0.370 3.730
7971 2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HB3 -0.374 3.134
7972
7973
7974
797545 contacts
7976
7977> hbonds :UNL showDist true radius 0.05 log true saveFile
7978> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
7979> WRM-16.hbonds.txt
7980
7981
7982 Finding intermodel H-bonds
7983 Finding intramodel H-bonds
7984 Constraints relaxed by 0.4 angstroms and 20 degrees
7985 Models used:
7986 1 2D3J.pdbqt
7987 2.1 2D3J--WRM-16.result.pdbqt
7988
7989 0 H-bonds
7990 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
7991
7992
7993
79940 hydrogen bonds found
7995
7996> select :UNL
7997
799828 atoms, 31 bonds, 1 residue, 1 model selected
7999
8000> label sel text "Ligand "
8001
8002> label height 1
8003
8004> ~select
8005
8006Nothing selected
8007
8008> 2dlabels text "Binding Energy: -6.9 kcal/mol" color red size 18 xpos .03
8009> ypos .95
8010
8011> 2dlabels text "2D3J WRM-16 Complex" color gray size 18 xpos .03 ypos .91
8012
8013> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
8014> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
8015> true
8016
8017> select :UNL
8018
801928 atoms, 31 bonds, 1 residue, 1 model selected
8020
8021> view sel
8022
8023> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
8024> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
8025> true
8026
8027> close
8028
8029> wait 5
8030
8031> set bgColor white
8032
8033> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2E50.pdbqt
8034
8035Chain information for 2E50.pdbqt #1
8036---
8037Chain | Description
8038A | No description available
8039B | No description available
8040P | No description available
8041Q | No description available
8042
8043Opened 2E50.pdbqt containing 1 structures (11470 atoms, 11602 bonds)
8044
8045> wait 5
8046
8047> hide surfaces
8048
8049> hide atoms
8050
8051> show cartoons
8052
8053> wait 5
8054
8055> addh
8056
8057Summary of feedback from adding hydrogens to 2E50.pdbqt #1
8058---
8059warning | Not adding hydrogens to /B MET 145 CB because it is missing heavy-
8060atom bond partners
8061notes | No usable SEQRES records for 2E50.pdbqt (#1) chain A; guessing termini
8062instead
8063No usable SEQRES records for 2E50.pdbqt (#1) chain B; guessing termini instead
8064No usable SEQRES records for 2E50.pdbqt (#1) chain P; guessing termini instead
8065No usable SEQRES records for 2E50.pdbqt (#1) chain Q; guessing termini instead
8066Chain-initial residues that are actual N termini: /A MET 1, /B SER 24, /P MET
80671, /Q SER 24
8068Chain-initial residues that are not actual N termini: /A ASP 21, /A SER 152,
8069/A PHE 189, /A ALA 201, /B SER 152, /B PHE 189, /B GLY 200, /P ALA 20, /P SER
8070152, /P PHE 189, /P GLY 200, /Q SER 152, /Q PHE 189, /Q ALA 201
8071Chain-final residues that are actual C termini: /A VAL 222, /B PRO 223, /P VAL
8072222, /Q PRO 223
8073Chain-final residues that are not actual C termini: /A SER 15, /A HIS 144, /A
8074MET 166, /A THR 194, /B MET 145, /B MET 166, /B THR 194, /P ASN 16, /P HIS
8075144, /P THR 167, /P THR 194, /Q HIS 144, /Q TRP 160, /Q THR 194
8076568 hydrogen bonds
8077Adding 'H' to /A ASP 21
8078Adding 'H' to /A SER 152
8079Adding 'H' to /A PHE 189
8080Adding 'H' to /A ALA 201
8081Adding 'H' to /B SER 152
80829 messages similar to the above omitted
8083/A SER 15 is not terminus, removing H atom from 'C'
8084/A HIS 144 is not terminus, removing H atom from 'C'
8085/A MET 166 is not terminus, removing H atom from 'C'
8086/A THR 194 is not terminus, removing H atom from 'C'
8087/B MET 145 is not terminus, removing H atom from 'C'
80889 messages similar to the above omitted
8089-41 hydrogens added
8090
8091
8092> wait 5
8093
8094> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2E50--
8095> WRM-16.result.pdbqt
8096
8097Summary of feedback from opening
8098/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2E50--WRM-16.result.pdbqt
8099---
8100warnings | Ignored bad PDB record found on line 2
8101REMARK VINA RESULT: -8.8 0.000 0.000
8102
8103Ignored bad PDB record found on line 3
8104REMARK 5 active torsions:
8105
8106Ignored bad PDB record found on line 4
8107REMARK status: ('A' for Active; 'I' for Inactive)
8108
8109Ignored bad PDB record found on line 5
8110REMARK 1 A between atoms: C_9 and O_15
8111
8112Ignored bad PDB record found on line 6
8113REMARK 2 A between atoms: C_10 and O_17
8114
8115184 messages similar to the above omitted
8116
8117Opened 2E50--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
8118bonds)
8119
8120> wait 5
8121
8122> close #2.2-9
8123
8124> wait 5
8125
8126> contacts :UNL radius 0.05 log true saveFile
8127> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
8128> WRM-16.contacts.txt
8129
8130
8131 Allowed overlap: -0.4
8132 H-bond overlap reduction: 0.4
8133 Ignore contacts between atoms separated by 4 bonds or less
8134 Detect intra-residue contacts: False
8135 Detect intra-molecule contacts: True
8136
8137 49 contacts
8138 atom1 atom2 overlap distance
8139 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 HB2 0.217 2.543
8140 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2E50.pdbqt #1/A PRO 214 HG1 0.160 2.720
8141 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 HN 0.145 2.735
8142 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O 2E50.pdbqt #1/A GLN 65 HB2 0.121 2.339
8143 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 HB1 0.092 2.668
8144 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 HD1 0.078 2.682
8145 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 O 0.052 3.308
8146 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 CD1 -0.046 3.506
8147 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2E50.pdbqt #1/A PRO 214 CG -0.080 3.660
8148 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASP 117 HN -0.136 2.896
8149 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 HB1 -0.144 3.024
8150 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O 2E50.pdbqt #1/A GLN 65 CB -0.152 3.312
8151 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 N -0.156 3.541
8152 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 CB -0.162 3.622
8153 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 HB2 -0.168 2.928
8154 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CE1 -0.182 3.642
8155 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 CB -0.188 3.768
8156 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 N -0.196 3.701
8157 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 HB1 -0.198 2.808
8158 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 HE1 -0.224 2.984
8159 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 HB1 -0.225 2.835
8160 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 HB1 -0.236 3.116
8161 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.245 3.705
8162 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 CB -0.258 3.718
8163 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.261 3.721
8164 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 NE -0.263 3.648
8165 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 CZ -0.277 3.737
8166 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CE2 -0.278 3.738
8167 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 NH1 -0.279 3.664
8168 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O 2E50.pdbqt #1/A ASN 61 O -0.292 3.232
8169 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 HD2 -0.294 3.054
8170 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 HN -0.296 3.056
8171 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 O -0.298 3.538
8172 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 HD2 -0.303 3.063
8173 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 OD1 -0.315 3.405
8174 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 N -0.318 3.703
8175 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 CB -0.319 3.899
8176 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 CD -0.323 3.783
8177 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2E50.pdbqt #1/A PRO 214 CB -0.323 3.903
8178 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 ND2 -0.330 3.835
8179 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 OD1 -0.332 3.422
8180 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CE2 -0.337 3.797
8181 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.340 3.650
8182 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 CA -0.362 3.942
8183 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 NE1 -0.364 3.749
8184 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.365 3.825
8185 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.379 3.839
8186 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 CB -0.383 3.843
8187 2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 NE1 -0.385 3.770
8188
8189
8190
819149 contacts
8192
8193> hbonds :UNL showDist true radius 0.05 log true saveFile
8194> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
8195> WRM-16.hbonds.txt
8196
8197
8198 Finding intermodel H-bonds
8199 Finding intramodel H-bonds
8200 Constraints relaxed by 0.4 angstroms and 20 degrees
8201 Models used:
8202 1 2E50.pdbqt
8203 2.1 2E50--WRM-16.result.pdbqt
8204
8205 0 H-bonds
8206 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
8207
8208
8209
82100 hydrogen bonds found
8211
8212> select :UNL
8213
821428 atoms, 31 bonds, 1 residue, 1 model selected
8215
8216> label sel text "Ligand "
8217
8218> label height 1
8219
8220> ~select
8221
8222Nothing selected
8223
8224> 2dlabels text "Binding Energy: -8.8 kcal/mol" color red size 18 xpos .03
8225> ypos .95
8226
8227> 2dlabels text "2E50 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
8228
8229> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
8230> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
8231> true
8232
8233> select :UNL
8234
823528 atoms, 31 bonds, 1 residue, 1 model selected
8236
8237> view sel
8238
8239> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
8240> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
8241> true
8242
8243> close
8244
8245> wait 5
8246
8247> set bgColor white
8248
8249> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5VBN.pdbqt
8250
8251Chain information for 5VBN.pdbqt #1
8252---
8253Chain | Description
8254A E | No description available
8255B F | No description available
8256
8257Opened 5VBN.pdbqt containing 1 structures (17529 atoms, 17769 bonds)
8258
8259> wait 5
8260
8261> hide surfaces
8262
8263> hide atoms
8264
8265> show cartoons
8266
8267> wait 5
8268
8269> addh
8270
8271Summary of feedback from adding hydrogens to 5VBN.pdbqt #1
8272---
8273notes | No usable SEQRES records for 5VBN.pdbqt (#1) chain A; guessing termini
8274instead
8275No usable SEQRES records for 5VBN.pdbqt (#1) chain B; guessing termini instead
8276No usable SEQRES records for 5VBN.pdbqt (#1) chain E; guessing termini instead
8277No usable SEQRES records for 5VBN.pdbqt (#1) chain F; guessing termini instead
8278Chain-initial residues that are actual N termini: /A HIS 84, /B SER 2150, /E
8279HIS 84, /F SER 2150
8280Chain-initial residues that are not actual N termini: /A PHE 163, /B PRO 2183,
8281/E PHE 163, /F PRO 2183
8282Chain-final residues that are actual C termini: /A PHE 527, /B PRO 2282, /E
8283PHE 527, /F PRO 2282
8284Chain-final residues that are not actual C termini: /A GLU 145, /B SER 2174,
8285/E GLU 145, /F SER 2174
8286854 hydrogen bonds
8287Adding 'H' to /A PHE 163
8288Adding 'H' to /E PHE 163
8289/A GLU 145 is not terminus, removing H atom from 'C'
8290/B SER 2174 is not terminus, removing H atom from 'C'
8291/E GLU 145 is not terminus, removing H atom from 'C'
8292/F SER 2174 is not terminus, removing H atom from 'C'
829335 hydrogens added
8294
8295
8296> wait 5
8297
8298> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VBN--
8299> WRM-16.result.pdbqt
8300
8301Summary of feedback from opening
8302/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VBN--WRM-16.result.pdbqt
8303---
8304warnings | Ignored bad PDB record found on line 2
8305REMARK VINA RESULT: -8.3 0.000 0.000
8306
8307Ignored bad PDB record found on line 3
8308REMARK 5 active torsions:
8309
8310Ignored bad PDB record found on line 4
8311REMARK status: ('A' for Active; 'I' for Inactive)
8312
8313Ignored bad PDB record found on line 5
8314REMARK 1 A between atoms: C_9 and O_15
8315
8316Ignored bad PDB record found on line 6
8317REMARK 2 A between atoms: C_10 and O_17
8318
8319184 messages similar to the above omitted
8320
8321Opened 5VBN--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
8322bonds)
8323
8324> wait 5
8325
8326> close #2.2-9
8327
8328> wait 5
8329
8330> contacts :UNL radius 0.05 log true saveFile
8331> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
8332> WRM-16.contacts.txt
8333
8334
8335 Allowed overlap: -0.4
8336 H-bond overlap reduction: 0.4
8337 Ignore contacts between atoms separated by 4 bonds or less
8338 Detect intra-residue contacts: False
8339 Detect intra-molecule contacts: True
8340
8341 63 contacts
8342 atom1 atom2 overlap distance
8343 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 190 1HD2 0.442 2.438
8344 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 HB2 0.235 2.525
8345 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 190 CD2 0.213 3.367
8346 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A GLN 189 O 0.052 3.308
8347 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HG2 0.023 2.737
8348 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 0.015 2.595
8349 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HB1 -0.011 2.621
8350 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 HG -0.027 2.787
8351 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A THR 188 3HG2 -0.054 2.814
8352 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HB1 -0.055 2.815
8353 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 -0.081 2.841
8354 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HA -0.095 2.855
8355 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CB -0.121 3.581
8356 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 -0.126 2.886
8357 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PHE 130 CZ -0.136 3.596
8358 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 HB1 -0.136 2.896
8359 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 -0.139 3.019
8360 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 HB1 -0.152 2.912
8361 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.156 3.616
8362 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A MET 186 CE -0.163 3.623
8363 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HD1 -0.168 3.048
8364 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 CB -0.173 3.633
8365 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 OG -0.175 3.555
8366 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HA -0.177 2.937
8367 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A GLN 189 C -0.183 3.763
8368 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CA -0.202 3.662
8369 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.204 3.664
8370 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CG -0.206 3.666
8371 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HB1 -0.216 2.826
8372 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 CB -0.222 3.682
8373 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 OG -0.228 3.488
8374 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 190 HA -0.229 3.109
8375 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 456 3HD1 -0.231 3.111
8376 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PHE 130 CE2 -0.231 3.691
8377 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A MET 186 HE2 -0.236 2.996
8378 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VBN.pdbqt #1/A GLU 220 OE2 -0.242 3.182
8379 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 HG -0.247 3.007
8380 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 3HD1 -0.254 3.014
8381 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A THR 188 HB -0.257 3.137
8382 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PHE 130 CE2 -0.260 3.720
8383 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CB -0.262 3.722
8384 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.265 3.725
8385 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.268 3.578
8386 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VBN.pdbqt #1/B LEU 2216 O -0.275 3.175
8387 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LYS 126 HE2 -0.301 3.181
8388 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB1 -0.303 3.063
8389 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CA -0.313 3.773
8390 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.313 3.773
8391 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 CB -0.323 3.783
8392 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A MET 186 HE2 -0.328 3.088
8393 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A THR 188 CG2 -0.330 3.790
8394 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A GLU 220 OE2 -0.346 3.586
8395 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 O -0.348 3.588
8396 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CB -0.353 3.663
8397 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HG2 -0.363 3.123
8398 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HE1 -0.366 2.976
8399 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HG2 -0.374 3.134
8400 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LYS 126 CE -0.382 3.962
8401 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CG -0.383 3.843
8402 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB1 -0.385 2.995
8403 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CG -0.387 3.847
8404 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CD1 -0.395 3.975
8405 5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 HB2 -0.398 3.158
8406
8407
8408
840963 contacts
8410
8411> hbonds :UNL showDist true radius 0.05 log true saveFile
8412> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
8413> WRM-16.hbonds.txt
8414
8415
8416 Finding intermodel H-bonds
8417 Finding intramodel H-bonds
8418 Constraints relaxed by 0.4 angstroms and 20 degrees
8419 Models used:
8420 1 5VBN.pdbqt
8421 2.1 5VBN--WRM-16.result.pdbqt
8422
8423 0 H-bonds
8424 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
8425
8426
8427
84280 hydrogen bonds found
8429
8430> select :UNL
8431
843228 atoms, 31 bonds, 1 residue, 1 model selected
8433
8434> label sel text "Ligand "
8435
8436> label height 1
8437
8438> ~select
8439
8440Nothing selected
8441
8442> 2dlabels text "Binding Energy: -8.3 kcal/mol" color red size 18 xpos .03
8443> ypos .95
8444
8445> 2dlabels text "5VBN WRM-16 Complex" color gray size 18 xpos .03 ypos .91
8446
8447> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
8448> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
8449> true
8450
8451> select :UNL
8452
845328 atoms, 31 bonds, 1 residue, 1 model selected
8454
8455> view sel
8456
8457> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
8458> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
8459> true
8460
8461> close
8462
8463> wait 5
8464
8465> set bgColor white
8466
8467> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3ALN.pdbqt
8468
8469Chain information for 3ALN.pdbqt #1
8470---
8471Chain | Description
8472A | No description available
8473B | No description available
8474C | No description available
8475
8476Opened 3ALN.pdbqt containing 1 structures (11428 atoms, 11539 bonds)
8477
8478> wait 5
8479
8480> hide surfaces
8481
8482> hide atoms
8483
8484> show cartoons
8485
8486> wait 5
8487
8488> addh
8489
8490Summary of feedback from adding hydrogens to 3ALN.pdbqt #1
8491---
8492warnings | Not adding hydrogens to /A SER 83 CB because it is missing heavy-
8493atom bond partners
8494Not adding hydrogens to /A LYS 86 CB because it is missing heavy-atom bond
8495partners
8496Not adding hydrogens to /A LYS 88 CB because it is missing heavy-atom bond
8497partners
8498Not adding hydrogens to /A LEU 105 C because it is missing heavy-atom bond
8499partners
8500Not adding hydrogens to /A ASP 138 CB because it is missing heavy-atom bond
8501partners
850230 messages similar to the above omitted
8503The following atoms were skipped as donors/acceptors due to missing heavy-atom
8504bond partners: /A PRO 308 N
8505notes | No usable SEQRES records for 3ALN.pdbqt (#1) chain A; guessing termini
8506instead
8507No usable SEQRES records for 3ALN.pdbqt (#1) chain B; guessing termini instead
8508No usable SEQRES records for 3ALN.pdbqt (#1) chain C; guessing termini instead
8509Chain-initial residues that are actual N termini: /A SER 83, /B SER 84, /C GLU
8510100
8511Chain-initial residues that are not actual N termini: /A TYR 284, /A THR 318,
8512/B TYR 284, /B ASP 324, /C ASN 117, /C ILE 127, /C CYS 158, /C CYS 174, /C LYS
8513231, /C SER 288, /C PRO 325
8514Chain-final residues that are actual C termini: /A PRO 389, /B ALA 390, /C ALA
8515390
8516Chain-final residues that are not actual C termini: /A GLN 253, /A TRP 310, /B
8517LEU 254, /B PRO 308, /C GLU 107, /C VAL 120, /C THR 136, /C TYR 165, /C LYS
8518224, /C PHE 248, /C PHE 305
8519465 hydrogen bonds
8520Adding 'H' to /A TYR 284
8521Adding 'H' to /A THR 318
8522Adding 'H' to /B TYR 284
8523Adding 'H' to /B ASP 324
8524Adding 'H' to /C ASN 117
85255 messages similar to the above omitted
8526/A GLN 253 is not terminus, removing H atom from 'C'
8527/A TRP 310 is not terminus, removing H atom from 'C'
8528/B LEU 254 is not terminus, removing H atom from 'C'
8529/B PRO 308 is not terminus, removing H atom from 'C'
8530/C GLU 107 is not terminus, removing H atom from 'C'
85316 messages similar to the above omitted
8532-6 hydrogens added
8533
8534
8535> wait 5
8536
8537> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3ALN--
8538> WRM-16.result.pdbqt
8539
8540Summary of feedback from opening
8541/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3ALN--WRM-16.result.pdbqt
8542---
8543warnings | Ignored bad PDB record found on line 2
8544REMARK VINA RESULT: -8.7 0.000 0.000
8545
8546Ignored bad PDB record found on line 3
8547REMARK 5 active torsions:
8548
8549Ignored bad PDB record found on line 4
8550REMARK status: ('A' for Active; 'I' for Inactive)
8551
8552Ignored bad PDB record found on line 5
8553REMARK 1 A between atoms: C_9 and O_15
8554
8555Ignored bad PDB record found on line 6
8556REMARK 2 A between atoms: C_10 and O_17
8557
8558184 messages similar to the above omitted
8559
8560Opened 3ALN--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
8561bonds)
8562
8563> wait 5
8564
8565> close #2.2-9
8566
8567> wait 5
8568
8569> contacts :UNL radius 0.05 log true saveFile
8570> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
8571> WRM-16.contacts.txt
8572
8573
8574 Allowed overlap: -0.4
8575 H-bond overlap reduction: 0.4
8576 Ignore contacts between atoms separated by 4 bonds or less
8577 Detect intra-residue contacts: False
8578 Detect intra-molecule contacts: True
8579
8580 50 contacts
8581 atom1 atom2 overlap distance
8582 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A TYR 113 HN 0.426 2.454
8583 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 0.385 2.375
8584 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 131 HE1 0.145 2.615
8585 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A THR 183 HA 0.134 2.626
8586 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 0.097 2.513
8587 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A TYR 113 N 0.090 3.415
8588 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A VAL 116 3HG2 0.087 2.523
8589 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 187 HE1 0.085 2.795
8590 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A LYS 131 HZ1 0.045 2.835
8591 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 1HG2 0.033 2.727
8592 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 0.027 2.733
8593 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A MET 181 O -0.005 3.245
8594 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 CA -0.019 3.479
8595 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LEU 236 3HD1 -0.024 2.904
8596 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 131 CE -0.041 3.501
8597 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A MET 178 SD -0.068 3.730
8598 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LEU 236 CD1 -0.070 3.650
8599 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A VAL 116 3HG2 -0.075 2.495
8600 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A SER 233 HG -0.104 2.864
8601 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 1HG2 -0.125 2.885
8602 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A ALA 112 N -0.153 3.658
8603 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 187 CE -0.159 3.739
8604 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 131 NZ -0.161 3.546
8605 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 CG2 -0.166 3.626
8606 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A LYS 131 NZ -0.194 3.699
8607 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 -0.208 2.968
8608 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A THR 183 CA -0.221 3.681
8609 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A ALA 129 CB -0.224 3.384
8610 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 1HG2 -0.224 2.984
8611 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 CG2 -0.237 3.697
8612 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A ALA 129 HB2 -0.237 2.697
8613 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 CA -0.248 3.558
8614 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 CA -0.257 3.717
8615 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A THR 183 HA -0.278 3.038
8616 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A SER 233 OG -0.287 2.807
8617 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A VAL 116 CG2 -0.305 3.615
8618 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A SER 233 OG -0.305 3.565
8619 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A GLY 114 N -0.308 3.813
8620 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ALA 112 HN -0.324 3.084
8621 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A VAL 116 CG2 -0.327 3.447
8622 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ALA 129 CB -0.329 3.909
8623 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 3HD1 -0.337 3.097
8624 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A ALA 112 HN -0.339 3.219
8625 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 2HD1 -0.352 3.112
8626 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LEU 236 2HD1 -0.353 3.233
8627 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A SER 182 O -0.357 3.597
8628 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 114 O -0.359 3.599
8629 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 CD1 -0.382 3.842
8630 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A VAL 116 3HG2 -0.398 3.008
8631 3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ALA 129 HB3 -0.400 3.280
8632
8633
8634
863550 contacts
8636
8637> hbonds :UNL showDist true radius 0.05 log true saveFile
8638> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
8639> WRM-16.hbonds.txt
8640
8641The following atoms were skipped as donors/acceptors due to missing heavy-atom
8642bond partners: 3ALN.pdbqt #1/A PRO 308 N
8643
8644
8645
8646 Finding intermodel H-bonds
8647 Finding intramodel H-bonds
8648 Constraints relaxed by 0.4 angstroms and 20 degrees
8649 Models used:
8650 1 3ALN.pdbqt
8651 2.1 3ALN--WRM-16.result.pdbqt
8652
8653 0 H-bonds
8654 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
8655
8656
8657
86580 hydrogen bonds found
8659
8660> select :UNL
8661
866228 atoms, 31 bonds, 1 residue, 1 model selected
8663
8664> label sel text "Ligand "
8665
8666> label height 1
8667
8668> ~select
8669
8670Nothing selected
8671
8672> 2dlabels text "Binding Energy: -8.7 kcal/mol" color red size 18 xpos .03
8673> ypos .95
8674
8675> 2dlabels text "3ALN WRM-16 Complex" color gray size 18 xpos .03 ypos .91
8676
8677> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
8678> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
8679> true
8680
8681> select :UNL
8682
868328 atoms, 31 bonds, 1 residue, 1 model selected
8684
8685> view sel
8686
8687> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
8688> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
8689> true
8690
8691> close
8692
8693> wait 5
8694
8695> set bgColor white
8696
8697> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1BJ8.pdbqt
8698
8699Chain information for 1BJ8.pdbqt #1
8700---
8701Chain | Description
8702A | No description available
8703
8704Opened 1BJ8.pdbqt containing 1 structures (1763 atoms, 1786 bonds)
8705
8706> wait 5
8707
8708> hide surfaces
8709
8710> hide atoms
8711
8712> show cartoons
8713
8714> wait 5
8715
8716> addh
8717
8718Summary of feedback from adding hydrogens to 1BJ8.pdbqt #1
8719---
8720notes | No usable SEQRES records for 1BJ8.pdbqt (#1) chain A; guessing termini
8721instead
8722Chain-initial residues that are actual N termini: /A MET 1
8723Chain-initial residues that are not actual N termini:
8724Chain-final residues that are actual C termini: /A ARG 109
8725Chain-final residues that are not actual C termini:
872653 hydrogen bonds
87271 hydrogens added
8728
8729
8730> wait 5
8731
8732> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1BJ8--
8733> WRM-16.result.pdbqt
8734
8735Summary of feedback from opening
8736/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1BJ8--WRM-16.result.pdbqt
8737---
8738warnings | Ignored bad PDB record found on line 2
8739REMARK VINA RESULT: -6.1 0.000 0.000
8740
8741Ignored bad PDB record found on line 3
8742REMARK 5 active torsions:
8743
8744Ignored bad PDB record found on line 4
8745REMARK status: ('A' for Active; 'I' for Inactive)
8746
8747Ignored bad PDB record found on line 5
8748REMARK 1 A between atoms: C_9 and O_15
8749
8750Ignored bad PDB record found on line 6
8751REMARK 2 A between atoms: C_10 and O_17
8752
8753184 messages similar to the above omitted
8754
8755Opened 1BJ8--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
8756bonds)
8757
8758> wait 5
8759
8760> close #2.2-9
8761
8762> wait 5
8763
8764> contacts :UNL radius 0.05 log true saveFile
8765> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
8766> WRM-16.contacts.txt
8767
8768
8769 Allowed overlap: -0.4
8770 H-bond overlap reduction: 0.4
8771 Ignore contacts between atoms separated by 4 bonds or less
8772 Detect intra-residue contacts: False
8773 Detect intra-molecule contacts: True
8774
8775 46 contacts
8776 atom1 atom2 overlap distance
8777 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HN 0.407 2.473
8778 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HD1 0.307 2.573
8779 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 CD1 0.188 3.392
8780 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 HD2 0.101 2.659
8781 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 HD2 0.099 2.661
8782 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TRP 94 HD1 0.093 2.367
8783 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 N 0.055 3.450
8784 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HB1 0.042 2.568
8785 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 HA 0.032 2.848
8786 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1BJ8.pdbqt #1/A TYR 93 HE1 0.021 2.859
8787 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A ARG 84 1HH1 -0.035 2.915
8788 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 HD1 -0.079 2.959
8789 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1BJ8.pdbqt #1/A TYR 93 CE1 -0.079 3.659
8790 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HD1 -0.085 2.965
8791 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A GLY 92 O -0.136 3.496
8792 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 CG -0.149 3.609
8793 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 CD -0.166 3.626
8794 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HD1 -0.172 2.782
8795 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 O -0.174 3.264
8796 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 1HH1 -0.175 2.235
8797 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 CE1 -0.177 3.487
8798 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HB1 -0.200 2.810
8799 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 HE1 -0.226 2.836
8800 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 O -0.231 3.471
8801 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 CB -0.254 3.714
8802 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A GLY 92 O -0.270 3.510
8803 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 CE1 -0.273 3.733
8804 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 CA -0.283 3.863
8805 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TRP 94 CD1 -0.288 3.448
8806 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 HZ2 -0.299 3.059
8807 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 HG2 -0.302 3.062
8808 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 CD -0.307 3.767
8809 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 91 O -0.315 3.555
8810 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 HB2 -0.317 2.777
8811 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 NH1 -0.328 3.013
8812 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HB1 -0.331 2.941
8813 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 CD -0.332 3.792
8814 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 HD1 -0.338 2.798
8815 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 HD2 -0.347 3.107
8816 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 CD1 -0.352 3.662
8817 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 CZ -0.358 3.478
8818 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 CB -0.364 3.524
8819 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 CB -0.372 3.682
8820 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A ARG 84 NH1 -0.385 3.890
8821 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 CA -0.392 3.552
8822 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 O -0.399 3.489
8823
8824
8825
882646 contacts
8827
8828> hbonds :UNL showDist true radius 0.05 log true saveFile
8829> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
8830> WRM-16.hbonds.txt
8831
8832
8833 Finding intermodel H-bonds
8834 Finding intramodel H-bonds
8835 Constraints relaxed by 0.4 angstroms and 20 degrees
8836 Models used:
8837 1 1BJ8.pdbqt
8838 2.1 1BJ8--WRM-16.result.pdbqt
8839
8840 1 H-bonds
8841 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
8842 1BJ8.pdbqt #1/A ARG 84 NH1 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 1HH1 3.013 2.235
8843
8844
8845
88461 hydrogen bonds found
8847
8848> select :UNL
8849
885028 atoms, 31 bonds, 1 residue, 1 model selected
8851
8852> label sel text "Ligand "
8853
8854> label height 1
8855
8856> ~select
8857
8858Nothing selected
8859
8860> 2dlabels text "Binding Energy: -6.1 kcal/mol" color red size 18 xpos .03
8861> ypos .95
8862
8863> 2dlabels text "1BJ8 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
8864
8865> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
8866> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
8867> true
8868
8869> select :UNL
8870
887128 atoms, 31 bonds, 1 residue, 1 model selected
8872
8873> view sel
8874
8875> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
8876> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
8877> true
8878
8879> close
8880
8881> wait 5
8882
8883> set bgColor white
8884
8885> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2LX7.pdbqt
8886
8887Chain information for 2LX7.pdbqt #1
8888---
8889Chain | Description
8890A | No description available
8891
8892Opened 2LX7.pdbqt containing 1 structures (931 atoms, 945 bonds)
8893
8894> wait 5
8895
8896> hide surfaces
8897
8898> hide atoms
8899
8900> show cartoons
8901
8902> wait 5
8903
8904> addh
8905
8906Summary of feedback from adding hydrogens to 2LX7.pdbqt #1
8907---
8908notes | No usable SEQRES records for 2LX7.pdbqt (#1) chain A; guessing termini
8909instead
8910Chain-initial residues that are actual N termini: /A MET 1
8911Chain-initial residues that are not actual N termini:
8912Chain-final residues that are actual C termini: /A LEU 60
8913Chain-final residues that are not actual C termini:
891424 hydrogen bonds
89150 hydrogens added
8916
8917
8918> wait 5
8919
8920> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LX7--
8921> WRM-16.result.pdbqt
8922
8923Summary of feedback from opening
8924/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LX7--WRM-16.result.pdbqt
8925---
8926warnings | Ignored bad PDB record found on line 2
8927REMARK VINA RESULT: -7.2 0.000 0.000
8928
8929Ignored bad PDB record found on line 3
8930REMARK 5 active torsions:
8931
8932Ignored bad PDB record found on line 4
8933REMARK status: ('A' for Active; 'I' for Inactive)
8934
8935Ignored bad PDB record found on line 5
8936REMARK 1 A between atoms: C_9 and O_15
8937
8938Ignored bad PDB record found on line 6
8939REMARK 2 A between atoms: C_10 and O_17
8940
8941184 messages similar to the above omitted
8942
8943Opened 2LX7--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
8944bonds)
8945
8946> wait 5
8947
8948> close #2.2-9
8949
8950> wait 5
8951
8952> contacts :UNL radius 0.05 log true saveFile
8953> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
8954> WRM-16.contacts.txt
8955
8956
8957 Allowed overlap: -0.4
8958 H-bond overlap reduction: 0.4
8959 Ignore contacts between atoms separated by 4 bonds or less
8960 Detect intra-residue contacts: False
8961 Detect intra-molecule contacts: True
8962
8963 35 contacts
8964 atom1 atom2 overlap distance
8965 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2LX7.pdbqt #1/A TRP 39 HH2 0.191 2.689
8966 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 HH 0.132 1.888
8967 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 HZ 0.130 2.750
8968 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 HH2 0.115 2.645
8969 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 O 0.112 3.128
8970 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HE2 0.053 2.707
8971 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 HG3 0.042 2.718
8972 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HH 0.010 2.600
8973 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2LX7.pdbqt #1/A TRP 39 CH2 -0.011 3.591
8974 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 HG3 -0.060 2.820
8975 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 CH2 -0.068 3.528
8976 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 HA3 -0.079 2.959
8977 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CZ -0.105 3.685
8978 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLU 15 O -0.118 3.058
8979 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 CA -0.132 3.712
8980 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 CE2 -0.179 3.639
8981 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 CZ3 -0.207 3.787
8982 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 HH2 -0.232 2.842
8983 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 CH2 -0.241 3.821
8984 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 HA2 -0.243 3.003
8985 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLU 15 O -0.254 3.154
8986 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CZ -0.296 3.606
8987 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 OH -0.300 2.820
8988 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 CG -0.319 3.779
8989 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 CG -0.323 3.783
8990 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 OH -0.323 3.583
8991 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 HE1 -0.324 2.934
8992 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 C -0.328 3.908
8993 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 CZ3 -0.350 3.810
8994 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLY 14 H -0.369 2.389
8995 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 CA -0.372 3.832
8996 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A SER 13 CB -0.376 3.496
8997 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 OH -0.387 3.497
8998 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CE1 -0.391 3.701
8999 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HE2 -0.398 3.008
9000
9001
9002
900335 contacts
9004
9005> hbonds :UNL showDist true radius 0.05 log true saveFile
9006> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
9007> WRM-16.hbonds.txt
9008
9009
9010 Finding intermodel H-bonds
9011 Finding intramodel H-bonds
9012 Constraints relaxed by 0.4 angstroms and 20 degrees
9013 Models used:
9014 1 2LX7.pdbqt
9015 2.1 2LX7--WRM-16.result.pdbqt
9016
9017 2 H-bonds
9018 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9019 2LX7.pdbqt #1/A GLY 14 N 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLY 14 H 3.315 2.389
9020 2LX7.pdbqt #1/A TYR 56 OH 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 HH 2.820 1.888
9021
9022
9023
90242 hydrogen bonds found
9025
9026> select :UNL
9027
902828 atoms, 31 bonds, 1 residue, 1 model selected
9029
9030> label sel text "Ligand "
9031
9032> label height 1
9033
9034> ~select
9035
9036Nothing selected
9037
9038> 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03
9039> ypos .95
9040
9041> 2dlabels text "2LX7 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
9042
9043> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
9044> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
9045> true
9046
9047> select :UNL
9048
904928 atoms, 31 bonds, 1 residue, 1 model selected
9050
9051> view sel
9052
9053> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
9054> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
9055> true
9056
9057> close
9058
9059> wait 5
9060
9061> set bgColor white
9062
9063> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1SM3.pdbqt
9064
9065Chain information for 1SM3.pdbqt #1
9066---
9067Chain | Description
9068H | No description available
9069L | No description available
9070P | No description available
9071
9072Opened 1SM3.pdbqt containing 1 structures (6388 atoms, 6469 bonds)
9073
9074> wait 5
9075
9076> hide surfaces
9077
9078> hide atoms
9079
9080> show cartoons
9081
9082> wait 5
9083
9084> addh
9085
9086Summary of feedback from adding hydrogens to 1SM3.pdbqt #1
9087---
9088warnings | Not adding hydrogens to /L ASP 41 CB because it is missing heavy-
9089atom bond partners
9090Not adding hydrogens to /L GLU 123 CB because it is missing heavy-atom bond
9091partners
9092Not adding hydrogens to /L GLN 163 CB because it is missing heavy-atom bond
9093partners
9094Not adding hydrogens to /H GLN 1 CB because it is missing heavy-atom bond
9095partners
9096Not adding hydrogens to /H GLU 42 CB because it is missing heavy-atom bond
9097partners
90987 messages similar to the above omitted
9099notes | No usable SEQRES records for 1SM3.pdbqt (#1) chain H; guessing termini
9100instead
9101No usable SEQRES records for 1SM3.pdbqt (#1) chain L; guessing termini instead
9102No usable SEQRES records for 1SM3.pdbqt (#1) chain P; guessing termini instead
9103Chain-initial residues that are actual N termini: /H GLN 1, /L ILE 3, /P SER 2
9104Chain-initial residues that are not actual N termini: /H SER 134
9105Chain-final residues that are actual C termini: /H ARG 213, /L ARG 208, /P PRO
910610
9107Chain-final residues that are not actual C termini: /H GLY 127
9108327 hydrogen bonds
9109Adding 'H' to /H SER 134
9110/H GLY 127 is not terminus, removing H atom from 'C'
91116 hydrogens added
9112
9113
9114> wait 5
9115
9116> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1SM3--
9117> WRM-16.result.pdbqt
9118
9119Summary of feedback from opening
9120/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1SM3--WRM-16.result.pdbqt
9121---
9122warnings | Ignored bad PDB record found on line 2
9123REMARK VINA RESULT: -7.7 0.000 0.000
9124
9125Ignored bad PDB record found on line 3
9126REMARK 5 active torsions:
9127
9128Ignored bad PDB record found on line 4
9129REMARK status: ('A' for Active; 'I' for Inactive)
9130
9131Ignored bad PDB record found on line 5
9132REMARK 1 A between atoms: C_9 and O_15
9133
9134Ignored bad PDB record found on line 6
9135REMARK 2 A between atoms: C_10 and O_17
9136
9137184 messages similar to the above omitted
9138
9139Opened 1SM3--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
9140bonds)
9141
9142> wait 5
9143
9144> close #2.2-9
9145
9146> wait 5
9147
9148> contacts :UNL radius 0.05 log true saveFile
9149> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
9150> WRM-16.contacts.txt
9151
9152
9153 Allowed overlap: -0.4
9154 H-bond overlap reduction: 0.4
9155 Ignore contacts between atoms separated by 4 bonds or less
9156 Detect intra-residue contacts: False
9157 Detect intra-molecule contacts: True
9158
9159 44 contacts
9160 atom1 atom2 overlap distance
9161 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H LEU 45 O 0.370 2.990
9162 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN 0.367 2.393
9163 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 0.353 2.257
9164 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 3HG2 0.128 2.632
9165 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 N 0.075 3.310
9166 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 2HG1 0.056 2.404
9167 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN 0.000 2.610
9168 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H ALA 60 HB1 -0.008 2.428
9169 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H ALA 60 HA -0.009 2.769
9170 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H TRP 47 HN -0.048 2.068
9171 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG1 -0.053 3.363
9172 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 3HG2 -0.115 2.995
9173 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.116 3.501
9174 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 HD1 -0.124 3.004
9175 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H GLU 46 HA -0.129 2.549
9176 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 -0.148 2.758
9177 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 3HG2 -0.173 2.933
9178 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L ILE 3 O -0.179 3.419
9179 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CG -0.185 3.645
9180 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN -0.187 2.797
9181 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 HA -0.215 2.635
9182 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L ILE 3 O -0.217 3.457
9183 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 -0.234 2.844
9184 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CE1 -0.246 3.706
9185 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 CG1 -0.256 3.416
9186 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CG -0.264 3.724
9187 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 HA -0.282 2.892
9188 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 CG2 -0.283 3.743
9189 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H ALA 60 CA -0.291 3.751
9190 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CE1 -0.319 3.779
9191 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H ALA 60 CB -0.325 3.445
9192 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L PHE 98 O -0.325 3.265
9193 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.328 3.713
9194 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 HG1 -0.347 2.957
9195 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 CG -0.354 3.664
9196 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H TRP 47 HN -0.354 2.964
9197 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 HG2 -0.363 3.243
9198 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.366 3.601
9199 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.369 3.874
9200 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG1 -0.375 3.685
9201 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 HA -0.380 3.140
9202 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 N -0.390 3.625
9203 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG2 -0.393 3.973
9204 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H GLU 46 CA -0.398 3.518
9205
9206
9207
920844 contacts
9209
9210> hbonds :UNL showDist true radius 0.05 log true saveFile
9211> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
9212> WRM-16.hbonds.txt
9213
9214
9215 Finding intermodel H-bonds
9216 Finding intramodel H-bonds
9217 Constraints relaxed by 0.4 angstroms and 20 degrees
9218 Models used:
9219 1 1SM3.pdbqt
9220 2.1 1SM3--WRM-16.result.pdbqt
9221
9222 1 H-bonds
9223 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9224 1SM3.pdbqt #1/H TRP 47 N 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H TRP 47 HN 3.052 2.068
9225
9226
9227
92281 hydrogen bonds found
9229
9230> select :UNL
9231
923228 atoms, 31 bonds, 1 residue, 1 model selected
9233
9234> label sel text "Ligand "
9235
9236> label height 1
9237
9238> ~select
9239
9240Nothing selected
9241
9242> 2dlabels text "Binding Energy: -7.7 kcal/mol" color red size 18 xpos .03
9243> ypos .95
9244
9245> 2dlabels text "1SM3 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
9246
9247> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
9248> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
9249> true
9250
9251> select :UNL
9252
925328 atoms, 31 bonds, 1 residue, 1 model selected
9254
9255> view sel
9256
9257> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
9258> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
9259> true
9260
9261> close
9262
9263> wait 5
9264
9265> set bgColor white
9266
9267> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1RRP.pdbqt
9268
9269Chain information for 1RRP.pdbqt #1
9270---
9271Chain | Description
9272A | No description available
9273B D | No description available
9274C | No description available
9275
9276Opened 1RRP.pdbqt containing 1 structures (10655 atoms, 10785 bonds)
9277
9278> wait 5
9279
9280> hide surfaces
9281
9282> hide atoms
9283
9284> show cartoons
9285
9286> wait 5
9287
9288> addh
9289
9290Summary of feedback from adding hydrogens to 1RRP.pdbqt #1
9291---
9292notes | No usable SEQRES records for 1RRP.pdbqt (#1) chain A; guessing termini
9293instead
9294No usable SEQRES records for 1RRP.pdbqt (#1) chain B; guessing termini instead
9295No usable SEQRES records for 1RRP.pdbqt (#1) chain C; guessing termini instead
9296No usable SEQRES records for 1RRP.pdbqt (#1) chain D; guessing termini instead
9297Chain-initial residues that are actual N termini: /A GLN 8, /B HIS 17, /C GLN
92988, /D HIS 17
9299Chain-initial residues that are not actual N termini:
9300Chain-final residues that are actual C termini: /A ASP 211, /B ILE 150, /C VAL
9301187, /D ILE 150
9302Chain-final residues that are not actual C termini:
9303454 hydrogen bonds
930412 hydrogens added
9305
9306
9307> wait 5
9308
9309> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RRP--
9310> WRM-16.result.pdbqt
9311
9312Summary of feedback from opening
9313/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RRP--WRM-16.result.pdbqt
9314---
9315warnings | Ignored bad PDB record found on line 2
9316REMARK VINA RESULT: -7.9 0.000 0.000
9317
9318Ignored bad PDB record found on line 3
9319REMARK 5 active torsions:
9320
9321Ignored bad PDB record found on line 4
9322REMARK status: ('A' for Active; 'I' for Inactive)
9323
9324Ignored bad PDB record found on line 5
9325REMARK 1 A between atoms: C_9 and O_15
9326
9327Ignored bad PDB record found on line 6
9328REMARK 2 A between atoms: C_10 and O_17
9329
9330184 messages similar to the above omitted
9331
9332Opened 1RRP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
9333bonds)
9334
9335> wait 5
9336
9337> close #2.2-9
9338
9339> wait 5
9340
9341> contacts :UNL radius 0.05 log true saveFile
9342> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
9343> WRM-16.contacts.txt
9344
9345
9346 Allowed overlap: -0.4
9347 H-bond overlap reduction: 0.4
9348 Ignore contacts between atoms separated by 4 bonds or less
9349 Detect intra-residue contacts: False
9350 Detect intra-molecule contacts: True
9351
9352 73 contacts
9353 atom1 atom2 overlap distance
9354 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 0.550 2.210
9355 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ALA 151 HB2 0.329 2.431
9356 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 HA2 0.286 2.594
9357 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 ND2 0.178 3.207
9358 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 CA 0.103 3.477
9359 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ 0.101 2.509
9360 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 0.066 2.694
9361 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HE1 0.052 2.708
9362 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 0.026 2.734
9363 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ 0.015 2.745
9364 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C ILE 126 1HD1 0.006 2.454
9365 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C THR 25 HG1 -0.002 2.882
9366 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HD2 -0.018 2.898
9367 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1RRP.pdbqt #1/C ILE 126 1HG2 -0.020 2.900
9368 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HB2 -0.024 2.784
9369 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ALA 151 CB -0.043 3.503
9370 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.053 2.663
9371 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.087 2.847
9372 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.100 2.710
9373 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.113 2.723
9374 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HG2 -0.115 2.875
9375 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.120 2.730
9376 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CE1 -0.126 3.586
9377 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HA -0.140 2.900
9378 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.150 3.030
9379 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1RRP.pdbqt #1/C ILE 126 CG2 -0.172 3.752
9380 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 CD -0.173 3.753
9381 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ1 -0.173 3.053
9382 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HZ3 -0.182 3.062
9383 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HB2 -0.189 2.949
9384 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.193 3.073
9385 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C THR 25 HG1 -0.195 2.255
9386 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CE1 -0.197 3.657
9387 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C THR 25 OG1 -0.198 3.578
9388 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.208 3.668
9389 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.213 2.973
9390 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CE -0.220 3.800
9391 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.220 3.680
9392 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.221 3.726
9393 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.225 3.685
9394 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.232 2.992
9395 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASP 125 OD1 -0.239 3.479
9396 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 -0.242 3.002
9397 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.254 3.564
9398 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.263 3.498
9399 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.264 3.724
9400 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.270 3.730
9401 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.272 2.882
9402 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 ND2 -0.275 3.660
9403 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HE1 -0.275 3.035
9404 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.277 3.587
9405 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CE -0.281 3.591
9406 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 CB -0.282 3.742
9407 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HG2 -0.293 3.053
9408 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.294 3.754
9409 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 NZ -0.297 3.802
9410 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.298 3.058
9411 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 N -0.311 3.816
9412 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.319 3.079
9413 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 N -0.321 3.706
9414 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CG -0.336 3.796
9415 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 1HG2 -0.341 2.951
9416 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.346 3.656
9417 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 37 O -0.351 3.441
9418 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CG -0.355 3.815
9419 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASP 125 OD1 -0.356 3.596
9420 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.358 3.118
9421 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 20 O -0.362 3.722
9422 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C ILE 126 CD1 -0.365 3.525
9423 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.372 3.832
9424 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CD -0.385 3.845
9425 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.393 3.628
9426 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.399 3.009
9427
9428
9429
943073 contacts
9431
9432> hbonds :UNL showDist true radius 0.05 log true saveFile
9433> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
9434> WRM-16.hbonds.txt
9435
9436
9437 Finding intermodel H-bonds
9438 Finding intramodel H-bonds
9439 Constraints relaxed by 0.4 angstroms and 20 degrees
9440 Models used:
9441 1 1RRP.pdbqt
9442 2.1 1RRP--WRM-16.result.pdbqt
9443
9444 1 H-bonds
9445 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9446 1RRP.pdbqt #1/C THR 25 OG1 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C THR 25 HG1 3.164 2.255
9447
9448
9449
94501 hydrogen bonds found
9451
9452> select :UNL
9453
945428 atoms, 31 bonds, 1 residue, 1 model selected
9455
9456> label sel text "Ligand "
9457
9458> label height 1
9459
9460> ~select
9461
9462Nothing selected
9463
9464> 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
9465> ypos .95
9466
9467> 2dlabels text "1RRP WRM-16 Complex" color gray size 18 xpos .03 ypos .91
9468
9469> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
9470> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
9471> true
9472
9473> select :UNL
9474
947528 atoms, 31 bonds, 1 residue, 1 model selected
9476
9477> view sel
9478
9479> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
9480> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
9481> true
9482
9483> close
9484
9485> wait 5
9486
9487> set bgColor white
9488
9489> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1OQD.pdbqt
9490
9491Chain information for 1OQD.pdbqt #1
9492---
9493Chain | Description
9494A B C D E F G H I J | No description available
9495K L M O P Q R | No description available
9496N | No description available
9497
9498Opened 1OQD.pdbqt containing 1 structures (27310 atoms, 27575 bonds)
9499
9500> wait 5
9501
9502> hide surfaces
9503
9504> hide atoms
9505
9506> show cartoons
9507
9508> wait 5
9509
9510> addh
9511
9512Summary of feedback from adding hydrogens to 1OQD.pdbqt #1
9513---
9514notes | No usable SEQRES records for 1OQD.pdbqt (#1) chain A; guessing termini
9515instead
9516No usable SEQRES records for 1OQD.pdbqt (#1) chain B; guessing termini instead
9517No usable SEQRES records for 1OQD.pdbqt (#1) chain C; guessing termini instead
9518No usable SEQRES records for 1OQD.pdbqt (#1) chain D; guessing termini instead
9519No usable SEQRES records for 1OQD.pdbqt (#1) chain E; guessing termini instead
952013 messages similar to the above omitted
9521Chain-initial residues that are actual N termini: /A VAL 1, /B VAL 1, /C VAL
95221, /D VAL 1, /E VAL 1, /F VAL 1, /G VAL 1, /H VAL 1, /I VAL 1, /J VAL 1, /K
9523CYS 1, /L CYS 1, /M CYS 1, /N CYS 1, /O CYS 1, /P CYS 1, /Q CYS 1, /R CYS 1
9524Chain-initial residues that are not actual N termini:
9525Chain-final residues that are actual C termini: /A LEU 144, /B LEU 144, /C LEU
9526144, /D LEU 144, /E LEU 144, /F LEU 144, /G LEU 144, /H LEU 144, /I LEU 144,
9527/J LEU 144, /K THR 39, /L THR 39, /M THR 39, /N CYS 21, /O THR 39, /P THR 39,
9528/Q THR 39, /R THR 39
9529Chain-final residues that are not actual C termini:
95301396 hydrogen bonds
953176 hydrogens added
9532
9533
9534> wait 5
9535
9536> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OQD--
9537> WRM-16.result.pdbqt
9538
9539Summary of feedback from opening
9540/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OQD--WRM-16.result.pdbqt
9541---
9542warnings | Ignored bad PDB record found on line 2
9543REMARK VINA RESULT: -8.0 0.000 0.000
9544
9545Ignored bad PDB record found on line 3
9546REMARK 5 active torsions:
9547
9548Ignored bad PDB record found on line 4
9549REMARK status: ('A' for Active; 'I' for Inactive)
9550
9551Ignored bad PDB record found on line 5
9552REMARK 1 A between atoms: C_9 and O_15
9553
9554Ignored bad PDB record found on line 6
9555REMARK 2 A between atoms: C_10 and O_17
9556
9557184 messages similar to the above omitted
9558
9559Opened 1OQD--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
9560bonds)
9561
9562> wait 5
9563
9564> close #2.2-9
9565
9566> wait 5
9567
9568> contacts :UNL radius 0.05 log true saveFile
9569> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
9570> WRM-16.contacts.txt
9571
9572
9573 Allowed overlap: -0.4
9574 H-bond overlap reduction: 0.4
9575 Ignore contacts between atoms separated by 4 bonds or less
9576 Detect intra-residue contacts: False
9577 Detect intra-molecule contacts: True
9578
9579 59 contacts
9580 atom1 atom2 overlap distance
9581 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HB2 0.581 2.179
9582 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 2HD2 0.325 2.555
9583 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CB 0.263 3.197
9584 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 HB1 0.221 2.659
9585 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 ND2 0.083 3.422
9586 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/B PRO 96 HA 0.046 2.374
9587 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 0.043 2.717
9588 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 HG1 0.040 2.720
9589 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 HG1 0.021 2.739
9590 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 O 0.012 3.348
9591 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 HB2 0.008 2.872
9592 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 OG1 -0.005 3.265
9593 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.011 3.101
9594 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/C GLU 97 HB2 -0.026 2.486
9595 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.055 2.665
9596 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HB2 -0.060 2.820
9597 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 HB1 -0.061 2.821
9598 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 CB -0.062 3.642
9599 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.072 2.682
9600 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 HG1 -0.076 2.956
9601 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CB -0.091 3.551
9602 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.093 2.853
9603 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.135 3.495
9604 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 OD1 -0.141 3.501
9605 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 C -0.144 3.724
9606 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 HB1 -0.150 2.610
9607 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C GLU 97 HN -0.158 2.768
9608 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CA -0.160 3.620
9609 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.168 2.778
9610 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.196 2.956
9611 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/B PRO 96 CA -0.202 3.322
9612 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HA -0.204 2.964
9613 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.212 3.452
9614 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A ASN 94 HB2 -0.215 2.975
9615 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 CB -0.218 3.798
9616 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.248 3.338
9617 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 CB -0.254 3.414
9618 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B ASN 94 O -0.260 3.500
9619 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.262 3.142
9620 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A ASN 94 CB -0.270 3.730
9621 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 CG -0.275 3.855
9622 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 O -0.277 3.517
9623 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 OG1 -0.281 3.541
9624 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CA -0.285 3.745
9625 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 HB2 -0.287 3.047
9626 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CG -0.291 3.751
9627 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CB -0.306 3.766
9628 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.316 3.076
9629 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.318 3.778
9630 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HA -0.322 3.082
9631 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CG -0.332 3.912
9632 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.340 3.800
9633 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.340 3.430
9634 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/C GLU 97 CB -0.345 3.465
9635 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 CG -0.346 3.506
9636 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C GLU 97 OE1 -0.350 3.710
9637 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 HG1 -0.351 2.811
9638 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B MET 95 C -0.360 3.820
9639 1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.383 3.843
9640
9641
9642
964359 contacts
9644
9645> hbonds :UNL showDist true radius 0.05 log true saveFile
9646> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
9647> WRM-16.hbonds.txt
9648
9649
9650 Finding intermodel H-bonds
9651 Finding intramodel H-bonds
9652 Constraints relaxed by 0.4 angstroms and 20 degrees
9653 Models used:
9654 1 1OQD.pdbqt
9655 2.1 1OQD--WRM-16.result.pdbqt
9656
9657 0 H-bonds
9658 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9659
9660
9661
96620 hydrogen bonds found
9663
9664> select :UNL
9665
966628 atoms, 31 bonds, 1 residue, 1 model selected
9667
9668> label sel text "Ligand "
9669
9670> label height 1
9671
9672> ~select
9673
9674Nothing selected
9675
9676> 2dlabels text "Binding Energy: -8.0 kcal/mol" color red size 18 xpos .03
9677> ypos .95
9678
9679> 2dlabels text "1OQD WRM-16 Complex" color gray size 18 xpos .03 ypos .91
9680
9681> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
9682> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
9683> true
9684
9685> select :UNL
9686
968728 atoms, 31 bonds, 1 residue, 1 model selected
9688
9689> view sel
9690
9691> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
9692> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
9693> true
9694
9695> close
9696
9697> wait 5
9698
9699> set bgColor white
9700
9701> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1S9J.pdbqt
9702
9703Chain information for 1S9J.pdbqt #1
9704---
9705Chain | Description
9706A | No description available
9707
9708Opened 1S9J.pdbqt containing 1 structures (4567 atoms, 4613 bonds)
9709
9710> wait 5
9711
9712> hide surfaces
9713
9714> hide atoms
9715
9716> show cartoons
9717
9718> wait 5
9719
9720> addh
9721
9722Summary of feedback from adding hydrogens to 1S9J.pdbqt #1
9723---
9724notes | No usable SEQRES records for 1S9J.pdbqt (#1) chain A; guessing termini
9725instead
9726Chain-initial residues that are actual N termini: /A MET 61
9727Chain-initial residues that are not actual N termini: /A VAL 224, /A PRO 306
9728Chain-final residues that are actual C termini: /A ASN 382
9729Chain-final residues that are not actual C termini: /A ALA 220, /A PHE 275
9730207 hydrogen bonds
9731Adding 'H' to /A VAL 224
9732/A ALA 220 is not terminus, removing H atom from 'C'
9733/A PHE 275 is not terminus, removing H atom from 'C'
9734-1 hydrogens added
9735
9736
9737> wait 5
9738
9739> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1S9J--
9740> WRM-16.result.pdbqt
9741
9742Summary of feedback from opening
9743/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1S9J--WRM-16.result.pdbqt
9744---
9745warnings | Ignored bad PDB record found on line 2
9746REMARK VINA RESULT: -9.2 0.000 0.000
9747
9748Ignored bad PDB record found on line 3
9749REMARK 5 active torsions:
9750
9751Ignored bad PDB record found on line 4
9752REMARK status: ('A' for Active; 'I' for Inactive)
9753
9754Ignored bad PDB record found on line 5
9755REMARK 1 A between atoms: C_9 and O_15
9756
9757Ignored bad PDB record found on line 6
9758REMARK 2 A between atoms: C_10 and O_17
9759
9760184 messages similar to the above omitted
9761
9762Opened 1S9J--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
9763bonds)
9764
9765> wait 5
9766
9767> close #2.2-9
9768
9769> wait 5
9770
9771> contacts :UNL radius 0.05 log true saveFile
9772> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
9773> WRM-16.contacts.txt
9774
9775
9776 Allowed overlap: -0.4
9777 H-bond overlap reduction: 0.4
9778 Ignore contacts between atoms separated by 4 bonds or less
9779 Detect intra-residue contacts: False
9780 Detect intra-molecule contacts: True
9781
9782 47 contacts
9783 atom1 atom2 overlap distance
9784 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 146 HN 0.179 2.581
9785 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 1HG1 0.131 2.329
9786 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A ASN 78 HB1 0.073 2.807
9787 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 149 HA1 0.062 2.818
9788 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 0.042 2.718
9789 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 HB2 0.034 2.846
9790 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ALA 95 CB 0.029 3.431
9791 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLN 153 OE1 0.015 3.345
9792 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.055 2.815
9793 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 HE1 -0.069 2.949
9794 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.092 3.552
9795 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 O -0.118 3.478
9796 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LYS 97 HE1 -0.119 2.999
9797 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A VAL 82 1HG2 -0.133 2.743
9798 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.148 3.608
9799 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A GLY 149 HA1 -0.156 2.616
9800 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 CE -0.158 3.278
9801 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ASP 208 OD2 -0.164 3.524
9802 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 149 CA -0.173 3.753
9803 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 146 N -0.179 3.564
9804 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 CE -0.181 3.761
9805 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A CYS 207 SG -0.191 3.853
9806 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 SD -0.205 3.747
9807 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A SER 194 HG -0.211 2.971
9808 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 HG -0.219 2.979
9809 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 CG1 -0.246 3.406
9810 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.247 3.707
9811 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.262 3.022
9812 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A SER 150 OG -0.269 2.789
9813 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A ASN 78 CB -0.271 3.851
9814 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 O -0.279 3.519
9815 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ASP 208 OD1 -0.291 3.651
9816 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A VAL 82 1HG2 -0.310 2.920
9817 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 HE2 -0.310 2.730
9818 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LYS 97 CE -0.316 3.896
9819 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A GLY 149 CA -0.320 3.480
9820 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 -0.323 3.083
9821 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 -0.326 2.936
9822 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.341 3.801
9823 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 CB -0.348 3.928
9824 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 CA -0.350 3.810
9825 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A LYS 192 NZ -0.352 3.857
9826 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.353 2.963
9827 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 2HD2 -0.368 3.128
9828 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A SER 194 HB2 -0.376 3.136
9829 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 2HD2 -0.385 3.145
9830 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 1HG2 -0.389 2.849
9831
9832
9833
983447 contacts
9835
9836> hbonds :UNL showDist true radius 0.05 log true saveFile
9837> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
9838> WRM-16.hbonds.txt
9839
9840
9841 Finding intermodel H-bonds
9842 Finding intramodel H-bonds
9843 Constraints relaxed by 0.4 angstroms and 20 degrees
9844 Models used:
9845 1 1S9J.pdbqt
9846 2.1 1S9J--WRM-16.result.pdbqt
9847
9848 1 H-bonds
9849 H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9850 1S9J.pdbqt #1/A LYS 97 NZ 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 HZ1 3.189 2.451
9851
9852
9853
98541 hydrogen bonds found
9855
9856> select :UNL
9857
985828 atoms, 31 bonds, 1 residue, 1 model selected
9859
9860> label sel text "Ligand "
9861
9862> label height 1
9863
9864> ~select
9865
9866Nothing selected
9867
9868> 2dlabels text "Binding Energy: -9.2 kcal/mol" color red size 18 xpos .03
9869> ypos .95
9870
9871> 2dlabels text "1S9J WRM-16 Complex" color gray size 18 xpos .03 ypos .91
9872
9873> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
9874> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
9875> true
9876
9877> select :UNL
9878
987928 atoms, 31 bonds, 1 residue, 1 model selected
9880
9881> view sel
9882
9883> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
9884> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
9885> true
9886
9887> close
9888
9889> wait 5
9890
9891> set bgColor white
9892
9893> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XJV.pdbqt
9894
9895Chain information for 1XJV.pdbqt #1
9896---
9897Chain | Description
9898A | No description available
9899B | No description available
9900
9901Opened 1XJV.pdbqt containing 1 structures (4991 atoms, 5066 bonds)
9902
9903> wait 5
9904
9905> hide surfaces
9906
9907> hide atoms
9908
9909> show cartoons
9910
9911> wait 5
9912
9913> addh
9914
9915Summary of feedback from adding hydrogens to 1XJV.pdbqt #1
9916---
9917notes | No usable SEQRES records for 1XJV.pdbqt (#1) chain A; guessing termini
9918instead
9919No usable SEQRES records for 1XJV.pdbqt (#1) chain B; guessing termini instead
9920Chain-initial residues that are actual N termini: /A ALA 6, /B DT 1
9921Chain-initial residues that are not actual N termini: /A THR 149
9922Chain-final residues that are actual C termini: /A ALA 299, /B DG 10
9923Chain-final residues that are not actual C termini: /A SER 145
9924244 hydrogen bonds
9925
9926Traceback (most recent call last):
9927File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9928packages/chimerax/cmd_line/tool.py", line 280, in execute
9929cmd.run(cmd_text)
9930File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9931packages/chimerax/core/commands/cli.py", line 2852, in run
9932result = ci.function(session, **kw_args)
9933File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9934packages/chimerax/open_command/cmd.py", line 118, in cmd_open
9935models = Command(session, registry=registry).run(provider_cmd_text,
9936log=log)[0]
9937File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9938packages/chimerax/core/commands/cli.py", line 2852, in run
9939result = ci.function(session, **kw_args)
9940File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9941packages/chimerax/open_command/cmd.py", line 179, in provider_open
9942models, status = collated_open(session, None, [data], data_format,
9943_add_models,
9944File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9945packages/chimerax/open_command/cmd.py", line 404, in collated_open
9946return func(*func_args, **func_kw)
9947File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9948packages/chimerax/core_formats/__init__.py", line 37, in open
9949return open_command_script(session, data, file_name)
9950File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9951packages/chimerax/core/scripting.py", line 161, in open_command_script
9952run(session, text)
9953File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9954packages/chimerax/core/commands/run.py", line 36, in run
9955results = command.run(text, log=log, return_json=return_json)
9956File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9957packages/chimerax/core/commands/cli.py", line 2852, in run
9958result = ci.function(session, **kw_args)
9959File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9960packages/chimerax/addh/cmd.py", line 63, in cmd_addh
9961add_h_func(session, structures, template=template, in_isolation=in_isolation,
9962**prot_schemes)
9963File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9964packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens
9965add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
9966hydrogen_totals,
9967File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9968packages/chimerax/addh/hbond.py", line 447, in add_hydrogens
9969did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
9970processed)
9971File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9972packages/chimerax/addh/hbond.py", line 1098, in _try_finish
9973pos = at_pos + nearest * h_len
9974TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
9975
9976TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
9977
9978File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
9979packages/chimerax/addh/hbond.py", line 1098, in _try_finish
9980pos = at_pos + nearest * h_len
9981
9982See log for complete Python traceback.
9983
9984
9985> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/ucsf-commands.cxc
9986
9987> set bgColor white
9988
9989> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3EI4.pdbqt
9990
9991Chain information for 3EI4.pdbqt #2
9992---
9993Chain | Description
9994A C E | No description available
9995B D F | No description available
9996
9997Opened 3EI4.pdbqt containing 1 structures (70284 atoms, 71031 bonds)
9998
9999> wait 5
10000
10001> hide surfaces
10002
10003> hide atoms
10004
10005> show cartoons
10006
10007> wait 5
10008
10009> addh
10010
10011Summary of feedback from adding hydrogens to multiple structures
10012---
10013notes | No usable SEQRES records for 1XJV.pdbqt (#1) chain A; guessing termini
10014instead
10015No usable SEQRES records for 1XJV.pdbqt (#1) chain B; guessing termini instead
10016Chain-initial residues that are actual N termini: 1XJV.pdbqt #1/A ALA 6,
100171XJV.pdbqt #1/B DT 1
10018Chain-initial residues that are not actual N termini: 1XJV.pdbqt #1/A THR 149
10019Chain-final residues that are actual C termini: 1XJV.pdbqt #1/A ALA 299,
100201XJV.pdbqt #1/B DG 10
10021Chain-final residues that are not actual C termini: 1XJV.pdbqt #1/A SER 145
10022244 hydrogen bonds
10023
10024Traceback (most recent call last):
10025File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10026packages/chimerax/cmd_line/tool.py", line 280, in execute
10027cmd.run(cmd_text)
10028File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10029packages/chimerax/core/commands/cli.py", line 2852, in run
10030result = ci.function(session, **kw_args)
10031File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10032packages/chimerax/open_command/cmd.py", line 118, in cmd_open
10033models = Command(session, registry=registry).run(provider_cmd_text,
10034log=log)[0]
10035File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10036packages/chimerax/core/commands/cli.py", line 2852, in run
10037result = ci.function(session, **kw_args)
10038File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10039packages/chimerax/open_command/cmd.py", line 179, in provider_open
10040models, status = collated_open(session, None, [data], data_format,
10041_add_models,
10042File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10043packages/chimerax/open_command/cmd.py", line 404, in collated_open
10044return func(*func_args, **func_kw)
10045File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10046packages/chimerax/core_formats/__init__.py", line 37, in open
10047return open_command_script(session, data, file_name)
10048File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10049packages/chimerax/core/scripting.py", line 161, in open_command_script
10050run(session, text)
10051File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10052packages/chimerax/core/commands/run.py", line 36, in run
10053results = command.run(text, log=log, return_json=return_json)
10054File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10055packages/chimerax/core/commands/cli.py", line 2852, in run
10056result = ci.function(session, **kw_args)
10057File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10058packages/chimerax/addh/cmd.py", line 63, in cmd_addh
10059add_h_func(session, structures, template=template, in_isolation=in_isolation,
10060**prot_schemes)
10061File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10062packages/chimerax/addh/cmd.py", line 162, in hbond_add_hydrogens
10063hbond_add_hydrogens(session, [struct], unknowns_info=unknowns_info,
10064File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10065packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens
10066add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
10067hydrogen_totals,
10068File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10069packages/chimerax/addh/hbond.py", line 447, in add_hydrogens
10070did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
10071processed)
10072File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10073packages/chimerax/addh/hbond.py", line 1098, in _try_finish
10074pos = at_pos + nearest * h_len
10075TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
10076
10077TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
10078
10079File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
10080packages/chimerax/addh/hbond.py", line 1098, in _try_finish
10081pos = at_pos + nearest * h_len
10082
10083See log for complete Python traceback.
10084
10085
10086
10087
10088
10089OpenGL version: 4.6 (Core Profile) Mesa 20.2.6
10090OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2)
10091OpenGL vendor: Intel
10092Manufacturer: HP
10093Model: HP Desktop Pro G1 MT
10094OS: Ubuntu 20.04 focal
10095Architecture: 64bit ELF
10096Virutal Machine: none
10097CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz
10098Cache Size: 9216 KB
10099Memory:
10100 total used free shared buff/cache available
10101 Mem: 11Gi 5.2Gi 2.7Gi 401Mi 3.7Gi 5.7Gi
10102 Swap: 31Gi 5.2Gi 26Gi
10103
10104Graphics:
10105 00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop) [8086:3e92]
10106 DeviceName: Onboard - Video
10107 Subsystem: Hewlett-Packard Company UHD Graphics 630 (Desktop) [103c:843c]
10108Locale: ('en_IN', 'ISO8859-1')
10109PyQt5 5.15.2, Qt 5.15.2
10110Installed Packages:
10111 alabaster: 0.7.12
10112 appdirs: 1.4.4
10113 Babel: 2.9.1
10114 backcall: 0.2.0
10115 blockdiag: 2.0.1
10116 certifi: 2020.12.5
10117 cftime: 1.5.0
10118 chardet: 3.0.4
10119 ChimeraX-AddCharge: 1.0.1
10120 ChimeraX-AddH: 2.1.6
10121 ChimeraX-AlignmentAlgorithms: 2.0
10122 ChimeraX-AlignmentHdrs: 3.2
10123 ChimeraX-AlignmentMatrices: 2.0
10124 ChimeraX-Alignments: 2.1
10125 ChimeraX-AmberInfo: 1.0
10126 ChimeraX-Arrays: 1.0
10127 ChimeraX-Atomic: 1.13.2
10128 ChimeraX-AtomicLibrary: 3.1.3
10129 ChimeraX-AtomSearch: 2.0
10130 ChimeraX-AtomSearchLibrary: 1.0
10131 ChimeraX-AxesPlanes: 2.0
10132 ChimeraX-BasicActions: 1.1
10133 ChimeraX-BILD: 1.0
10134 ChimeraX-BlastProtein: 1.1
10135 ChimeraX-BondRot: 2.0
10136 ChimeraX-BugReporter: 1.0
10137 ChimeraX-BuildStructure: 2.5.2
10138 ChimeraX-Bumps: 1.0
10139 ChimeraX-BundleBuilder: 1.1
10140 ChimeraX-ButtonPanel: 1.0
10141 ChimeraX-CageBuilder: 1.0
10142 ChimeraX-CellPack: 1.0
10143 ChimeraX-Centroids: 1.1
10144 ChimeraX-ChemGroup: 2.0
10145 ChimeraX-Clashes: 2.1
10146 ChimeraX-ColorActions: 1.0
10147 ChimeraX-ColorGlobe: 1.0
10148 ChimeraX-ColorKey: 1.2.1
10149 ChimeraX-CommandLine: 1.1.4
10150 ChimeraX-ConnectStructure: 2.0
10151 ChimeraX-Contacts: 1.0
10152 ChimeraX-Core: 1.2.5
10153 ChimeraX-CoreFormats: 1.0
10154 ChimeraX-coulombic: 1.1.1
10155 ChimeraX-Crosslinks: 1.0
10156 ChimeraX-Crystal: 1.0
10157 ChimeraX-CrystalContacts: 1.0
10158 ChimeraX-DataFormats: 1.1
10159 ChimeraX-Dicom: 1.0
10160 ChimeraX-DistMonitor: 1.1.3
10161 ChimeraX-DistUI: 1.0
10162 ChimeraX-Dssp: 2.0
10163 ChimeraX-EMDB-SFF: 1.0
10164 ChimeraX-ExperimentalCommands: 1.0
10165 ChimeraX-FileHistory: 1.0
10166 ChimeraX-FunctionKey: 1.0
10167 ChimeraX-Geometry: 1.1
10168 ChimeraX-gltf: 1.0
10169 ChimeraX-Graphics: 1.0
10170 ChimeraX-Hbonds: 2.1
10171 ChimeraX-Help: 1.1
10172 ChimeraX-HKCage: 1.3
10173 ChimeraX-IHM: 1.0
10174 ChimeraX-ImageFormats: 1.1
10175 ChimeraX-IMOD: 1.0
10176 ChimeraX-IO: 1.0.1
10177 ChimeraX-Label: 1.0
10178 ChimeraX-LinuxSupport: 1.0
10179 ChimeraX-ListInfo: 1.1.1
10180 ChimeraX-Log: 1.1.2
10181 ChimeraX-LookingGlass: 1.1
10182 ChimeraX-Maestro: 1.8.1
10183 ChimeraX-Map: 1.0.2
10184 ChimeraX-MapData: 2.0
10185 ChimeraX-MapEraser: 1.0
10186 ChimeraX-MapFilter: 2.0
10187 ChimeraX-MapFit: 2.0
10188 ChimeraX-MapSeries: 2.0
10189 ChimeraX-Markers: 1.0
10190 ChimeraX-Mask: 1.0
10191 ChimeraX-MatchMaker: 1.2.1
10192 ChimeraX-MDcrds: 2.2
10193 ChimeraX-MedicalToolbar: 1.0.1
10194 ChimeraX-Meeting: 1.0
10195 ChimeraX-MLP: 1.1
10196 ChimeraX-mmCIF: 2.3
10197 ChimeraX-MMTF: 2.1
10198 ChimeraX-Modeller: 1.0.1
10199 ChimeraX-ModelPanel: 1.0.1
10200 ChimeraX-ModelSeries: 1.0
10201 ChimeraX-Mol2: 2.0
10202 ChimeraX-Morph: 1.0
10203 ChimeraX-MouseModes: 1.1
10204 ChimeraX-Movie: 1.0
10205 ChimeraX-Neuron: 1.0
10206 ChimeraX-Nucleotides: 2.0.1
10207 ChimeraX-OpenCommand: 1.5
10208 ChimeraX-PDB: 2.4.1
10209 ChimeraX-PDBBio: 1.0
10210 ChimeraX-PDBLibrary: 1.0.1
10211 ChimeraX-PDBMatrices: 1.0
10212 ChimeraX-PickBlobs: 1.0
10213 ChimeraX-Positions: 1.0
10214 ChimeraX-PresetMgr: 1.0.1
10215 ChimeraX-PubChem: 2.0.1
10216 ChimeraX-ReadPbonds: 1.0
10217 ChimeraX-Registration: 1.1
10218 ChimeraX-RemoteControl: 1.0
10219 ChimeraX-ResidueFit: 1.0
10220 ChimeraX-RestServer: 1.1
10221 ChimeraX-RNALayout: 1.0
10222 ChimeraX-RotamerLibMgr: 2.0
10223 ChimeraX-RotamerLibsDunbrack: 2.0
10224 ChimeraX-RotamerLibsDynameomics: 2.0
10225 ChimeraX-RotamerLibsRichardson: 2.0
10226 ChimeraX-SaveCommand: 1.4
10227 ChimeraX-SchemeMgr: 1.0
10228 ChimeraX-SDF: 2.0
10229 ChimeraX-Segger: 1.0
10230 ChimeraX-Segment: 1.0
10231 ChimeraX-SeqView: 2.3
10232 ChimeraX-Shape: 1.0.1
10233 ChimeraX-Shell: 1.0
10234 ChimeraX-Shortcuts: 1.0
10235 ChimeraX-ShowAttr: 1.0
10236 ChimeraX-ShowSequences: 1.0
10237 ChimeraX-SideView: 1.0
10238 ChimeraX-Smiles: 2.0.1
10239 ChimeraX-SmoothLines: 1.0
10240 ChimeraX-SpaceNavigator: 1.0
10241 ChimeraX-StdCommands: 1.3.1
10242 ChimeraX-STL: 1.0
10243 ChimeraX-Storm: 1.0
10244 ChimeraX-Struts: 1.0
10245 ChimeraX-Surface: 1.0
10246 ChimeraX-SwapAA: 2.0
10247 ChimeraX-SwapRes: 2.1
10248 ChimeraX-TapeMeasure: 1.0
10249 ChimeraX-Test: 1.0
10250 ChimeraX-Toolbar: 1.0.1
10251 ChimeraX-ToolshedUtils: 1.2
10252 ChimeraX-Tug: 1.0
10253 ChimeraX-UI: 1.7.6
10254 ChimeraX-uniprot: 2.1
10255 ChimeraX-UnitCell: 1.0
10256 ChimeraX-ViewDockX: 1.0
10257 ChimeraX-Vive: 1.1
10258 ChimeraX-VolumeMenu: 1.0
10259 ChimeraX-VTK: 1.0
10260 ChimeraX-WavefrontOBJ: 1.0
10261 ChimeraX-WebCam: 1.0
10262 ChimeraX-WebServices: 1.0
10263 ChimeraX-Zone: 1.0
10264 colorama: 0.4.3
10265 comtypes: 1.1.7
10266 cxservices: 1.0
10267 cycler: 0.10.0
10268 Cython: 0.29.21
10269 decorator: 5.0.9
10270 distlib: 0.3.1
10271 distro: 1.5.0
10272 docutils: 0.16
10273 filelock: 3.0.12
10274 funcparserlib: 0.3.6
10275 grako: 3.16.5
10276 h5py: 2.10.0
10277 html2text: 2020.1.16
10278 idna: 2.10
10279 ihm: 0.17
10280 imagecodecs: 2020.5.30
10281 imagesize: 1.2.0
10282 ipykernel: 5.3.4
10283 ipython: 7.18.1
10284 ipython-genutils: 0.2.0
10285 jedi: 0.17.2
10286 Jinja2: 2.11.2
10287 jupyter-client: 6.1.7
10288 jupyter-core: 4.7.1
10289 kiwisolver: 1.3.1
10290 line-profiler: 2.1.2
10291 lxml: 4.6.2
10292 lz4: 3.1.0
10293 MarkupSafe: 2.0.1
10294 matplotlib: 3.3.2
10295 msgpack: 1.0.0
10296 netCDF4: 1.5.4
10297 networkx: 2.5
10298 numexpr: 2.7.3
10299 numpy: 1.19.2
10300 numpydoc: 1.1.0
10301 openvr: 1.14.1501
10302 packaging: 20.9
10303 ParmEd: 3.2.0
10304 parso: 0.7.1
10305 pexpect: 4.8.0
10306 pickleshare: 0.7.5
10307 Pillow: 7.2.0
10308 pip: 21.0.1
10309 pkginfo: 1.5.0.1
10310 prompt-toolkit: 3.0.18
10311 psutil: 5.7.2
10312 ptyprocess: 0.7.0
10313 pycollada: 0.7.1
10314 pydicom: 2.0.0
10315 Pygments: 2.7.1
10316 PyOpenGL: 3.1.5
10317 PyOpenGL-accelerate: 3.1.5
10318 pyparsing: 2.4.7
10319 PyQt5-commercial: 5.15.2
10320 PyQt5-sip: 12.8.1
10321 PyQtWebEngine-commercial: 5.15.2
10322 python-dateutil: 2.8.1
10323 pytz: 2021.1
10324 pyzmq: 22.0.3
10325 qtconsole: 4.7.7
10326 QtPy: 1.9.0
10327 RandomWords: 0.3.0
10328 requests: 2.24.0
10329 scipy: 1.5.2
10330 setuptools: 50.3.2
10331 sfftk-rw: 0.6.7.dev1
10332 six: 1.15.0
10333 snowballstemmer: 2.1.0
10334 sortedcontainers: 2.2.2
10335 Sphinx: 3.2.1
10336 sphinxcontrib-applehelp: 1.0.2
10337 sphinxcontrib-blockdiag: 2.0.0
10338 sphinxcontrib-devhelp: 1.0.2
10339 sphinxcontrib-htmlhelp: 2.0.0
10340 sphinxcontrib-jsmath: 1.0.1
10341 sphinxcontrib-qthelp: 1.0.3
10342 sphinxcontrib-serializinghtml: 1.1.5
10343 suds-jurko: 0.6
10344 tables: 3.6.1
10345 tifffile: 2020.9.3
10346 tinyarray: 1.2.3
10347 tornado: 6.1
10348 traitlets: 5.0.5
10349 urllib3: 1.25.11
10350 wcwidth: 0.2.5
10351 webcolors: 1.11.1
10352 wheel: 0.36.0
10353 wheel-filename: 1.2.0
10354
10355}}}