[Chimera-users] Small molecules and antechamber
Jon Rumbley
jrumbley at d.umn.edu
Wed Jul 28 08:03:52 PDT 2010
I have several small organic molecules constructed in ChemDraw and converted
in Chem3D to .mol2 files. I can open them in Chimera but cannot seem to add
charges to. I was simply using the add charge menu commands and AM1-BCC and
assuming the structures would be read as nonstandard but antechamber reports
an error with residue ****. The error log has no real indication of what the
trouble might be. Are there additional steps I must take before assigning
charges? The structures already have hydrogens added. An example .mol2 file
is below:
@<TRIPOS>MOLECULE
****
44 45 1 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 C -2.8306 2.5311 -0.9622 C.2 1 ****
0.0000
2 C -2.8728 1.1718 -1.0363 C.2 1 ****
0.0000
3 C -4.0552 0.3840 -0.9622 C.1 1 ****
0.0000
4 C -1.6082 0.4134 -1.1450 C.2 1 ****
0.0000
5 N -5.0052 -0.2769 -0.8917 N.1 1 ****
0.0000
6 O -1.8883 -0.9222 -1.2800 O.3 1 ****
0.0000
7 O -0.4722 0.8459 -1.1451 O.2 1 ****
0.0000
8 C -0.8034 -1.8901 -1.1282 C.3 1 ****
0.0000
9 C -0.3965 -1.8485 0.3585 C.2 1 ****
0.0000
10 C -1.4383 -3.2075 -1.5077 C.3 1 ****
0.0000
11 N 0.6925 -2.6041 0.6991 N.am 1 ****
0.0000
12 O -1.0062 -1.1536 1.1745 O.2 1 ****
0.0000
13 C 1.2426 -2.6055 2.0833 C.3 1 ****
0.0000
14 C 2.4273 -3.5343 2.1380 C.ar 1 ****
0.0000
15 C -3.9592 3.4353 -0.8741 C.ar 1 ****
0.0000
16 C -3.7802 4.6664 -0.1923 C.ar 1 ****
0.0000
17 C -4.8234 5.5702 -0.0757 C.ar 1 ****
0.0000
18 C -6.0611 5.2454 -0.6673 C.ar 1 ****
0.0000
19 C -6.2633 4.0447 -1.3692 C.ar 1 ****
0.0000
20 C -5.2063 3.1490 -1.4690 C.ar 1 ****
0.0000
21 O -7.0408 6.1768 -0.5154 O.3 1 ****
0.0000
22 C 3.5525 -3.2801 1.3388 C.ar 1 ****
0.0000
23 C 4.6333 -4.1642 1.3545 C.ar 1 ****
0.0000
24 C 4.6017 -5.2952 2.1768 C.ar 1 ****
0.0000
25 C 3.4888 -5.5395 2.9865 C.ar 1 ****
0.0000
26 C 2.3994 -4.6635 2.9668 C.ar 1 ****
0.0000
27 H -1.8332 3.0176 -0.9495 H 1 ****
0.0000
28 H 0.0351 -1.5845 -1.7993 H 1 ****
0.0000
29 H -0.6942 -4.0150 -1.5686 H 1 ****
0.0000
30 H -1.9272 -3.1457 -2.4932 H 1 ****
0.0000
31 H -2.2150 -3.5214 -0.7935 H 1 ****
0.0000
32 H 1.1669 -3.2048 0.0167 H 1 ****
0.0000
33 H 1.5395 -1.5662 2.3712 H 1 ****
0.0000
34 H 0.4439 -2.9024 2.8058 H 1 ****
0.0000
35 H -2.8085 4.9012 0.2576 H 1 ****
0.0000
36 H -4.7042 6.5169 0.4530 H 1 ****
0.0000
37 H -7.2285 3.8279 -1.8322 H 1 ****
0.0000
38 H -5.3406 2.2282 -2.0442 H 1 ****
0.0000
39 H -7.9024 5.8992 -0.9622 H 1 ****
0.0000
40 H 3.5844 -2.3950 0.7014 H 1 ****
0.0000
41 H 5.5045 -3.9710 0.7250 H 1 ****
0.0000
42 H 5.4465 -5.9867 2.1870 H 1 ****
0.0000
43 H 3.4659 -6.4183 3.6333 H 1 ****
0.0000
44 H 1.5299 -4.8643 3.5946 H 1 ****
0.0000
@<TRIPOS>BOND
1 1 2 2
2 1 15 1
3 1 27 1
4 2 3 1
5 2 4 1
6 3 5 3
7 4 6 1
8 4 7 2
9 6 8 1
10 8 9 1
11 8 10 1
12 8 28 1
13 9 11 1
14 9 12 2
15 10 29 1
16 10 30 1
17 10 31 1
18 11 13 1
19 11 32 1
20 13 14 1
21 13 33 1
22 13 34 1
23 14 22 2
24 14 26 1
25 15 16 2
26 15 20 1
27 16 17 1
28 16 35 1
29 17 18 2
30 17 36 1
31 18 19 1
32 18 21 1
33 19 20 2
34 19 37 1
35 20 38 1
36 21 39 1
37 22 23 1
38 22 40 1
39 23 24 2
40 23 41 1
41 24 25 1
42 24 42 1
43 25 26 2
44 25 43 1
45 26 44 1
Thanks for any help you can provide.
Dr. Jon N. Rumbley
Assistant Professor
Dept. of Pharmacy Practice and Pharmaceutical Sciences
University of Minnesota-Duluth
127 LSci
1110 Kirby Dr.
Duluth, MN 55812
Phone: 218-726-6047
email: jrumbley at d.umn.edu
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