The following bug report has been submitted:
Platform: Linux-5.10.0-1034-oem-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/ucsf-commands.cxc
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3EI4.pdbqt
Chain information for 3EI4.pdbqt #1
---
Chain | Description
A C E | No description available
B D F | No description available
Opened 3EI4.pdbqt containing 1 structures (70284 atoms, 71031 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 3EI4.pdbqt #1
---
warnings | Not adding hydrogens to /A GLU 368 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A ARG 369 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLN 759 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLU 779 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A THR 780 CB because it is missing heavy-atom bond
partners
49 messages similar to the above omitted
notes | No usable SEQRES records for 3EI4.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 3EI4.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 3EI4.pdbqt (#1) chain C; guessing termini instead
No usable SEQRES records for 3EI4.pdbqt (#1) chain D; guessing termini instead
No usable SEQRES records for 3EI4.pdbqt (#1) chain E; guessing termini instead
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A MET 1, /B TRP 54, /C MET
1, /D TRP 54, /E MET 1, /F TRP 54
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A HIS 1140, /B GLU 421, /C
HIS 1140, /D GLU 421, /E HIS 1140, /F GLU 421
Chain-final residues that are not actual C termini:
2812 hydrogen bonds
114 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3EI4--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3EI4--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.8 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 3EI4--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.1 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1BJ8 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2LX7.pdbqt
Chain information for 2LX7.pdbqt #1
---
Chain | Description
A | No description available
Opened 2LX7.pdbqt containing 1 structures (931 atoms, 945 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2LX7.pdbqt #1
---
notes | No usable SEQRES records for 2LX7.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LEU 60
Chain-final residues that are not actual C termini:
24 hydrogen bonds
0 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LX7--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LX7--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.2 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2LX7--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
35 contacts
atom1 atom2 overlap distance
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2LX7.pdbqt #1/A TRP 39 HH2 0.191 2.689
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 HH 0.132 1.888
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 HZ 0.130 2.750
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 HH2 0.115 2.645
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 O 0.112 3.128
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HE2 0.053 2.707
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 HG3 0.042 2.718
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HH 0.010 2.600
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2LX7.pdbqt #1/A TRP 39 CH2 -0.011 3.591
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 HG3 -0.060 2.820
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 CH2 -0.068 3.528
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 HA3 -0.079 2.959
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CZ -0.105 3.685
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLU 15 O -0.118 3.058
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 CA -0.132 3.712
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 CE2 -0.179 3.639
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 CZ3 -0.207 3.787
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 HH2 -0.232 2.842
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 CH2 -0.241 3.821
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 HA2 -0.243 3.003
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLU 15 O -0.254 3.154
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CZ -0.296 3.606
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 OH -0.300 2.820
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 CG -0.319 3.779
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 CG -0.323 3.783
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 OH -0.323 3.583
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 HE1 -0.324 2.934
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 C -0.328 3.908
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 CZ3 -0.350 3.810
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLY 14 H -0.369 2.389
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 CA -0.372 3.832
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A SER 13 CB -0.376 3.496
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 OH -0.387 3.497
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CE1 -0.391 3.701
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HE2 -0.398 3.008
35 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2LX7.pdbqt
2.1 2LX7--WRM-16.result.pdbqt
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
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
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
2 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2LX7 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1SM3.pdbqt
Chain information for 1SM3.pdbqt #1
---
Chain | Description
H | No description available
L | No description available
P | No description available
Opened 1SM3.pdbqt containing 1 structures (6388 atoms, 6469 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1SM3.pdbqt #1
---
warnings | Not adding hydrogens to /L ASP 41 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /L GLU 123 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /L GLN 163 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /H GLN 1 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /H GLU 42 CB because it is missing heavy-atom bond
partners
7 messages similar to the above omitted
notes | No usable SEQRES records for 1SM3.pdbqt (#1) chain H; guessing termini
instead
No usable SEQRES records for 1SM3.pdbqt (#1) chain L; guessing termini instead
No usable SEQRES records for 1SM3.pdbqt (#1) chain P; guessing termini instead
Chain-initial residues that are actual N termini: /H GLN 1, /L ILE 3, /P SER 2
Chain-initial residues that are not actual N termini: /H SER 134
Chain-final residues that are actual C termini: /H ARG 213, /L ARG 208, /P PRO
10
Chain-final residues that are not actual C termini: /H GLY 127
327 hydrogen bonds
Adding 'H' to /H SER 134
/H GLY 127 is not terminus, removing H atom from 'C'
6 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1SM3--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1SM3--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.7 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1SM3--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
44 contacts
atom1 atom2 overlap distance
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H LEU 45 O 0.370 2.990
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN 0.367 2.393
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 0.353 2.257
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 3HG2 0.128 2.632
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 N 0.075 3.310
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 2HG1 0.056 2.404
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN 0.000 2.610
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H ALA 60 HB1 -0.008 2.428
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H ALA 60 HA -0.009 2.769
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H TRP 47 HN -0.048 2.068
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG1 -0.053 3.363
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 3HG2 -0.115 2.995
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.116 3.501
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 HD1 -0.124 3.004
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H GLU 46 HA -0.129 2.549
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 -0.148 2.758
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 3HG2 -0.173 2.933
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L ILE 3 O -0.179 3.419
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CG -0.185 3.645
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN -0.187 2.797
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 HA -0.215 2.635
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L ILE 3 O -0.217 3.457
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 -0.234 2.844
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CE1 -0.246 3.706
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 CG1 -0.256 3.416
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CG -0.264 3.724
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 HA -0.282 2.892
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 CG2 -0.283 3.743
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H ALA 60 CA -0.291 3.751
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CE1 -0.319 3.779
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H ALA 60 CB -0.325 3.445
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L PHE 98 O -0.325 3.265
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.328 3.713
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 HG1 -0.347 2.957
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 CG -0.354 3.664
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H TRP 47 HN -0.354 2.964
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 HG2 -0.363 3.243
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.366 3.601
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.369 3.874
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG1 -0.375 3.685
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 HA -0.380 3.140
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 N -0.390 3.625
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG2 -0.393 3.973
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H GLU 46 CA -0.398 3.518
44 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1SM3.pdbqt
2.1 1SM3--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
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
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.7 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1SM3 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1RRP.pdbqt
Chain information for 1RRP.pdbqt #1
---
Chain | Description
A | No description available
B D | No description available
C | No description available
Opened 1RRP.pdbqt containing 1 structures (10655 atoms, 10785 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1RRP.pdbqt #1
---
notes | No usable SEQRES records for 1RRP.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1RRP.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 1RRP.pdbqt (#1) chain C; guessing termini instead
No usable SEQRES records for 1RRP.pdbqt (#1) chain D; guessing termini instead
Chain-initial residues that are actual N termini: /A GLN 8, /B HIS 17, /C GLN
8, /D HIS 17
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASP 211, /B ILE 150, /C VAL
187, /D ILE 150
Chain-final residues that are not actual C termini:
454 hydrogen bonds
12 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RRP--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RRP--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.9 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1RRP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
73 contacts
atom1 atom2 overlap distance
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 0.550 2.210
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ALA 151 HB2 0.329 2.431
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 HA2 0.286 2.594
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 ND2 0.178 3.207
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 CA 0.103 3.477
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ 0.101 2.509
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 0.066 2.694
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HE1 0.052 2.708
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 0.026 2.734
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ 0.015 2.745
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C ILE 126 1HD1 0.006 2.454
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C THR 25 HG1 -0.002 2.882
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HD2 -0.018 2.898
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1RRP.pdbqt #1/C ILE 126 1HG2 -0.020 2.900
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HB2 -0.024 2.784
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ALA 151 CB -0.043 3.503
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.053 2.663
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.087 2.847
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.100 2.710
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.113 2.723
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HG2 -0.115 2.875
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.120 2.730
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CE1 -0.126 3.586
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HA -0.140 2.900
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.150 3.030
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1RRP.pdbqt #1/C ILE 126 CG2 -0.172 3.752
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 CD -0.173 3.753
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ1 -0.173 3.053
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HZ3 -0.182 3.062
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HB2 -0.189 2.949
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.193 3.073
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C THR 25 HG1 -0.195 2.255
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CE1 -0.197 3.657
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C THR 25 OG1 -0.198 3.578
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.208 3.668
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.213 2.973
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CE -0.220 3.800
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.220 3.680
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.221 3.726
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.225 3.685
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.232 2.992
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASP 125 OD1 -0.239 3.479
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 -0.242 3.002
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.254 3.564
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.263 3.498
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.264 3.724
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.270 3.730
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.272 2.882
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 ND2 -0.275 3.660
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HE1 -0.275 3.035
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.277 3.587
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CE -0.281 3.591
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 CB -0.282 3.742
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HG2 -0.293 3.053
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.294 3.754
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 NZ -0.297 3.802
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.298 3.058
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 N -0.311 3.816
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.319 3.079
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 N -0.321 3.706
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CG -0.336 3.796
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 1HG2 -0.341 2.951
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.346 3.656
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 37 O -0.351 3.441
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CG -0.355 3.815
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASP 125 OD1 -0.356 3.596
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.358 3.118
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 20 O -0.362 3.722
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C ILE 126 CD1 -0.365 3.525
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.372 3.832
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CD -0.385 3.845
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.393 3.628
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.399 3.009
73 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1RRP.pdbqt
2.1 1RRP--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
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
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1RRP WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1OQD.pdbqt
Chain information for 1OQD.pdbqt #1
---
Chain | Description
A B C D E F G H I J | No description available
K L M O P Q R | No description available
N | No description available
Opened 1OQD.pdbqt containing 1 structures (27310 atoms, 27575 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1OQD.pdbqt #1
---
notes | No usable SEQRES records for 1OQD.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1OQD.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 1OQD.pdbqt (#1) chain C; guessing termini instead
No usable SEQRES records for 1OQD.pdbqt (#1) chain D; guessing termini instead
No usable SEQRES records for 1OQD.pdbqt (#1) chain E; guessing termini instead
13 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A VAL 1, /B VAL 1, /C VAL
1, /D VAL 1, /E VAL 1, /F VAL 1, /G VAL 1, /H VAL 1, /I VAL 1, /J VAL 1, /K
CYS 1, /L CYS 1, /M CYS 1, /N CYS 1, /O CYS 1, /P CYS 1, /Q CYS 1, /R CYS 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LEU 144, /B LEU 144, /C LEU
144, /D LEU 144, /E LEU 144, /F LEU 144, /G LEU 144, /H LEU 144, /I LEU 144,
/J LEU 144, /K THR 39, /L THR 39, /M THR 39, /N CYS 21, /O THR 39, /P THR 39,
/Q THR 39, /R THR 39
Chain-final residues that are not actual C termini:
1396 hydrogen bonds
76 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OQD--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OQD--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.0 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1OQD--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
59 contacts
atom1 atom2 overlap distance
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HB2 0.581 2.179
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 2HD2 0.325 2.555
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CB 0.263 3.197
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 HB1 0.221 2.659
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 ND2 0.083 3.422
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/B PRO 96 HA 0.046 2.374
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 0.043 2.717
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 HG1 0.040 2.720
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 HG1 0.021 2.739
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 O 0.012 3.348
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 HB2 0.008 2.872
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 OG1 -0.005 3.265
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.011 3.101
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/C GLU 97 HB2 -0.026 2.486
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.055 2.665
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HB2 -0.060 2.820
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 HB1 -0.061 2.821
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 CB -0.062 3.642
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.072 2.682
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 HG1 -0.076 2.956
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CB -0.091 3.551
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.093 2.853
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.135 3.495
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 OD1 -0.141 3.501
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 C -0.144 3.724
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 HB1 -0.150 2.610
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C GLU 97 HN -0.158 2.768
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CA -0.160 3.620
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.168 2.778
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.196 2.956
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/B PRO 96 CA -0.202 3.322
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HA -0.204 2.964
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.212 3.452
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A ASN 94 HB2 -0.215 2.975
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 CB -0.218 3.798
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.248 3.338
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 CB -0.254 3.414
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B ASN 94 O -0.260 3.500
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.262 3.142
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A ASN 94 CB -0.270 3.730
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 CG -0.275 3.855
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 O -0.277 3.517
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 OG1 -0.281 3.541
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CA -0.285 3.745
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 HB2 -0.287 3.047
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CG -0.291 3.751
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CB -0.306 3.766
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.316 3.076
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.318 3.778
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HA -0.322 3.082
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CG -0.332 3.912
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.340 3.800
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.340 3.430
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/C GLU 97 CB -0.345 3.465
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 CG -0.346 3.506
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C GLU 97 OE1 -0.350 3.710
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 HG1 -0.351 2.811
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B MET 95 C -0.360 3.820
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.383 3.843
59 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1OQD.pdbqt
2.1 1OQD--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.0 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1OQD WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1S9J.pdbqt
Chain information for 1S9J.pdbqt #1
---
Chain | Description
A | No description available
Opened 1S9J.pdbqt containing 1 structures (4567 atoms, 4613 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1S9J.pdbqt #1
---
notes | No usable SEQRES records for 1S9J.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A MET 61
Chain-initial residues that are not actual N termini: /A VAL 224, /A PRO 306
Chain-final residues that are actual C termini: /A ASN 382
Chain-final residues that are not actual C termini: /A ALA 220, /A PHE 275
207 hydrogen bonds
Adding 'H' to /A VAL 224
/A ALA 220 is not terminus, removing H atom from 'C'
/A PHE 275 is not terminus, removing H atom from 'C'
-1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1S9J--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1S9J--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -9.2 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1S9J--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
47 contacts
atom1 atom2 overlap distance
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 146 HN 0.179 2.581
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 1HG1 0.131 2.329
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A ASN 78 HB1 0.073 2.807
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 149 HA1 0.062 2.818
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 0.042 2.718
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 HB2 0.034 2.846
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ALA 95 CB 0.029 3.431
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLN 153 OE1 0.015 3.345
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.055 2.815
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 HE1 -0.069 2.949
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.092 3.552
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 O -0.118 3.478
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LYS 97 HE1 -0.119 2.999
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A VAL 82 1HG2 -0.133 2.743
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.148 3.608
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A GLY 149 HA1 -0.156 2.616
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 CE -0.158 3.278
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ASP 208 OD2 -0.164 3.524
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 149 CA -0.173 3.753
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 146 N -0.179 3.564
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 CE -0.181 3.761
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A CYS 207 SG -0.191 3.853
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 SD -0.205 3.747
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A SER 194 HG -0.211 2.971
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 HG -0.219 2.979
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 CG1 -0.246 3.406
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.247 3.707
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.262 3.022
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A SER 150 OG -0.269 2.789
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A ASN 78 CB -0.271 3.851
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 O -0.279 3.519
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ASP 208 OD1 -0.291 3.651
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A VAL 82 1HG2 -0.310 2.920
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 HE2 -0.310 2.730
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LYS 97 CE -0.316 3.896
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A GLY 149 CA -0.320 3.480
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 -0.323 3.083
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 -0.326 2.936
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.341 3.801
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 CB -0.348 3.928
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 CA -0.350 3.810
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A LYS 192 NZ -0.352 3.857
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.353 2.963
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 2HD2 -0.368 3.128
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A SER 194 HB2 -0.376 3.136
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 2HD2 -0.385 3.145
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 1HG2 -0.389 2.849
47 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1S9J.pdbqt
2.1 1S9J--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
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
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -9.2 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1S9J WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XJV.pdbqt
Chain information for 1XJV.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 1XJV.pdbqt containing 1 structures (4991 atoms, 5066 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1XJV.pdbqt #1
---
notes | No usable SEQRES records for 1XJV.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1XJV.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A ALA 6, /B DT 1
Chain-initial residues that are not actual N termini: /A THR 149
Chain-final residues that are actual C termini: /A ALA 299, /B DG 10
Chain-final residues that are not actual C termini: /A SER 145
244 hydrogen bonds
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 404, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 37, in open
return open_command_script(session, data, file_name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/scripting.py", line 161, in open_command_script
run(session, text)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 447, in add_hydrogens
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 1098, in _try_finish
pos = at_pos + nearest * h_len
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 1098, in _try_finish
pos = at_pos + nearest * h_len
See log for complete Python traceback.
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/ucsf-commands.cxc
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3EI4.pdbqt
Chain information for 3EI4.pdbqt #2
---
Chain | Description
A C E | No description available
B D F | No description available
Opened 3EI4.pdbqt containing 1 structures (70284 atoms, 71031 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 1XJV.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1XJV.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: 1XJV.pdbqt #1/A ALA 6,
1XJV.pdbqt #1/B DT 1
Chain-initial residues that are not actual N termini: 1XJV.pdbqt #1/A THR 149
Chain-final residues that are actual C termini: 1XJV.pdbqt #1/A ALA 299,
1XJV.pdbqt #1/B DG 10
Chain-final residues that are not actual C termini: 1XJV.pdbqt #1/A SER 145
244 hydrogen bonds
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 404, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 37, in open
return open_command_script(session, data, file_name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/scripting.py", line 161, in open_command_script
run(session, text)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 162, in hbond_add_hydrogens
hbond_add_hydrogens(session, [struct], unknowns_info=unknowns_info,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 447, in add_hydrogens
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 1098, in _try_finish
pos = at_pos + nearest * h_len
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 1098, in _try_finish
pos = at_pos + nearest * h_len
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 20.2.6
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel
Manufacturer: HP
Model: HP Desktop Pro G1 MT
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz
Cache Size: 9216 KB
Memory:
total used free shared buff/cache available
Mem: 11Gi 5.2Gi 2.7Gi 401Mi 3.7Gi 5.7Gi
Swap: 31Gi 5.2Gi 26Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop) [8086:3e92]
DeviceName: Onboard - Video
Subsystem: Hewlett-Packard Company UHD Graphics 630 (Desktop) [103c:843c]
Locale: ('en_IN', 'ISO8859-1')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Had to delete middle section of log to meet maximum size limit for Trac description. Full log is attached.