[gmx-users] Installing topolbuild
Bruce D. Ray
brucedray at yahoo.com
Fri May 29 17:52:37 CEST 2009
On Friday, May 29, 2009 9:38:00 AM, vivek sharma <viveksharma.iitb at gmail.com> wrote:
> Thanks a lot for your quick response. It is really encouraging to get response from developers like you.
>
> I tried generating topology again with the same command line and corrected input file. This time I am
> getting error as
>
_________________
> Fatal error.
> Source code file: readmol2.c, line: 693
> Atom 4 (N) has 3 connections when allowed 0
> --------------------------------------------------------
>
> I tried with different forcefield but getting the same error. Is
there any misake on my part or
> molecule structure or topolbuild can't
handle such files ?
>
> Please suggest if there is some other option for generating topology files from structure files.
I'm sorry. I had missed this before. Is there some reason why the
types of the C and N atoms are incomplete? Where did this file
come from? The absence of correct atom types is indeed an error.
All carbons must have a complete type that is one of
C.3, C.2, C.cat , C.ar, or C.1
All nitrogens must have a complete type that is one of
N.3, N.2, N.1, N.ar, N.pl3, N.am, or N.4
All oxygens must have a complete type that is one of
O.3, O.2, or O.co2
All sulfurs must have a complete type that is one of
S.3, S.2, S.o, or S.o2
The only phosphorous type is P.3
The only other sub-typed elements have the types
Co.oh, Cr.oh, and Cr.th
topolbuild can handle syntactically correct mol2 files. The key phrase is
syntactically correct. It means that the file must match the definition for
mol2 files given by Tripos in terms of atom types, as well as bond types
and format. topolbuild uses the Tripos atom types as part of the
assignment of gaff, amber, gromacs, or (version 1.3 now in testing)
oplsaa atom types.
I have tried to guess at the correct Tripos atom types for your molecule
based on the bonding and I attach that below. These may not be absolutely
correct. However, this does generate a topology with topolbuild.
@<TRIPOS>MOLECULE
Bromo-WR99210.pdb
42 43 0 0 0
SMALL
GASTEIGER
Energy = 0
@<TRIPOS>ATOM
1 BR 3.8280 5.3090 11.2220 Br 1 UNK1 -0.0503
2 O 0.1390 1.8570 3.5110 O.3 1 UNK1 -0.2127
3 O 2.3680 3.2800 5.7230 O.3 1 UNK1 -0.4919
4 N -0.7270 2.5300 2.6710 N.pl3 1 UNK1 -0.0823
5 N -2.7920 2.6890 1.3630 N.ar 1 UNK1 -0.0643
6 N -1.1590 4.4210 1.3650 N.ar 1 UNK1 -0.0011
7 N 0.8240 4.2680 2.6030 N.pl3 1 UNK1 -0.2863
8 N -3.1550 4.6100 0.1360 N.pl3 1 UNK1 -0.2859
9 C -1.9520 1.8810 2.2650 C.3 1 UNK1 0.2652
10 C -2.8030 1.5760 3.5030 C.3 1 UNK1 0.0108
11 C -1.6250 0.5840 1.5150 C.3 1 UNK1 0.0108
12 C -0.3810 3.7610 2.1840 C.2 1 UNK1 0.4233
13 C -0.2000 2.2550 4.8340 C.3 1 UNK1 0.0932
14 C 0.7110 1.5570 5.8320 C.3 1 UNK1 0.0086
15 C -2.3690 3.8600 0.9790 C.2 1 UNK1 0.4286
16 C 2.1760 1.8790 5.5870 C.3 1 UNK1 0.0918
17 C 2.7000 3.7400 6.9700 C.ar 1 UNK1 0.1206
18 C 3.4230 2.9260 7.8350 C.ar 1 UNK1 -0.0189
19 C 2.3110 5.0170 7.3580 C.ar 1 UNK1 -0.0189
20 C 3.7590 3.3940 9.1050 C.ar 1 UNK1 -0.0443
21 C 2.6470 5.4860 8.6280 C.ar 1 UNK1 -0.0443
22 C 3.3720 4.6740 9.5020 C.ar 1 UNK1 0.0181
23 H -2.3890 0.7640 4.1100 H 1 UNK1 0.0301
24 H -3.7980 1.2280 3.1950 H 1 UNK1 0.0301
25 H -2.9770 2.4700 4.1120 H 1 UNK1 0.0301
26 H -2.5380 0.0750 1.1850 H 1 UNK1 0.0301
27 H -1.0580 -0.1150 2.1400 H 1 UNK1 0.0301
28 H -1.0240 0.7890 0.6210 H 1 UNK1 0.0301
29 H -1.2070 1.9930 5.1370 H 1 UNK1 0.0600
30 H -0.1050 3.3420 4.9500 H 1 UNK1 0.0600
31 H 0.5760 0.4730 5.7420 H 1 UNK1 0.0321
32 H 0.4220 1.8490 6.8470 H 1 UNK1 0.0321
33 H 2.8170 1.2260 6.1790 H 1 UNK1 0.0697
34 H 2.4370 1.6350 4.5500 H 1 UNK1 0.0697
35 H 1.1470 5.1760 2.2890 H 1 UNK1 0.2547
36 H 1.4470 3.7330 3.1970 H 1 UNK1 0.2547
37 H -2.8590 5.5250 -0.1840 H 1 UNK1 0.2548
38 H -4.0520 4.2670 -0.1900 H 1 UNK1 0.2548
39 H 3.8150 1.9500 7.5800 H 1 UNK1 0.0654
40 H 1.7450 5.6510 6.6810 H 1 UNK1 0.0654
41 H 4.3360 2.7560 9.7690 H 1 UNK1 0.0630
42 H 2.3370 6.4850 8.9220 H 1 UNK1 0.0630
@<TRIPOS>BOND
1 1 22 1
2 2 4 1
3 2 13 1
4 3 16 1
5 3 17 1
6 4 9 1
7 4 12 1
8 5 9 1
9 5 15 2
10 6 12 2
11 6 15 1
12 7 12 1
13 7 35 1
14 7 36 1
15 8 15 1
16 8 37 1
17 8 38 1
18 9 10 1
19 9 11 1
20 10 23 1
21 10 24 1
22 10 25 1
23 11 26 1
24 11 27 1
25 11 28 1
26 13 14 1
27 13 29 1
28 13 30 1
29 14 16 1
30 14 31 1
31 14 32 1
32 16 33 1
33 16 34 1
34 17 18 ar
35 17 19 ar
36 18 20 ar
37 18 39 1
38 19 21 ar
39 19 40 1
40 20 22 ar
41 20 41 1
42 21 22 ar
43 21 42 1
@<TRIPOS>
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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