[gmx-users] Fatal error: Atomtype 'OS' not found!
Yunfeng Hu
yunfeng at scripps.edu
Thu Oct 7 00:27:33 CEST 2004
However, everything is fine if cocaine.itp alone without protein is
used in the simulation. Here is what it looks like:
[ moleculetype ]
;name nrexcl
COC 3
;
;
; This file was generated by PRODRG version 040913.0519
; PRODRG written/copyrighted by Daan van Aalten
;
; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ atoms ]
; nr type resnr resid atom cgnr charge
1 CH3 1 COC C1 1 0.078
2 OS 1 COC O5 1 -0.110
3 C 1 COC C6 1 0.531
4 O 1 COC O7 1 -0.499
5 CH1 1 COC C8 2 0.127
6 CH1 1 COC C10 2 0.127
7 NL 1 COC N12 2 -0.300
8 CH3 1 COC C14 2 0.046
9 CH2 1 COC C18 3 0.000
10 CH2 1 COC C21 3 0.000
11 CH1 1 COC C24 4 0.000
12 CH2 1 COC C26 5 0.100
13 CS1 1 COC C29 5 0.258
14 OS 1 COC O1 5 -0.141
15 C 1 COC C2 5 0.418
16 O 1 COC O3 5 -0.635
17 CB 1 COC C4 6 0.015
18 CR61 1 COC C5 6 -0.007
19 CR61 1 COC C7 6 -0.008
20 CR61 1 COC C9 7 0.000
21 CR61 1 COC C11 7 0.000
22 CR61 1 COC C13 7 0.000
[ bonds ]
;ai aj fu c0 c1
1 2 1 0.143 251040.0 0.143 251040.0 ; C1 O5
2 3 1 0.136 376560.0 0.136 376560.0 ; O5 C6
3 4 1 0.123 502080.0 0.123 502080.0 ; C6 O7
3 5 1 0.153 334720.0 0.153 334720.0 ; C6 C8
5 6 1 0.153 334720.0 0.153 334720.0 ; C8 C10
5 13 1 0.153 334720.0 0.153 334720.0 ; C8 C29
6 7 1 0.147 376560.0 0.147 376560.0 ; C10 N12
6 9 1 0.153 334720.0 0.153 334720.0 ; C10 C18
7 8 1 0.147 376560.0 0.147 376560.0 ; N12 C14
7 11 1 0.147 376560.0 0.147 376560.0 ; N12 C24
9 10 1 0.153 334720.0 0.153 334720.0 ; C18 C21
10 11 1 0.153 334720.0 0.153 334720.0 ; C21 C24
11 12 1 0.153 334720.0 0.153 334720.0 ; C24 C26
12 13 1 0.153 251040.0 0.153 251040.0 ; C26 C29
13 14 1 0.144 251040.0 0.144 251040.0 ; C29 O1
14 15 1 0.136 376560.0 0.136 376560.0 ; O1 C2
15 16 1 0.123 502080.0 0.123 502080.0 ; C2 O3
15 17 1 0.153 334720.0 0.153 334720.0 ; C2 C4
17 18 1 0.139 418400.0 0.139 418400.0 ; C4 C5
17 22 1 0.139 418400.0 0.139 418400.0 ; C4 C13
18 19 1 0.139 418400.0 0.139 418400.0 ; C5 C7
19 20 1 0.139 418400.0 0.139 418400.0 ; C7 C9
20 21 1 0.139 418400.0 0.139 418400.0 ; C9 C11
21 22 1 0.139 418400.0 0.139 418400.0 ; C11 C13
[ pairs ]
;ai aj fu c0 c1
1 4 1 ; C1 O7
1 5 1 ; C1 C8
2 6 1 ; O5 C10
2 13 1 ; O5 C29
3 7 1 ; C6 N12
3 9 1 ; C6 C18
3 12 1 ; C6 C26
3 14 1 ; C6 O1
4 6 1 ; O7 C10
4 13 1 ; O7 C29
5 8 1 ; C8 C14
5 10 1 ; C8 C21
5 11 1 ; C8 C24
5 15 1 ; C8 C2
6 12 1 ; C10 C26
6 14 1 ; C10 O1
7 13 1 ; N12 C29
8 9 1 ; C14 C18
8 10 1 ; C14 C21
8 12 1 ; C14 C26
9 12 1 ; C18 C26
9 13 1 ; C18 C29
10 13 1 ; C21 C29
11 14 1 ; C24 O1
12 15 1 ; C26 C2
13 16 1 ; C29 O3
13 17 1 ; C29 C4
14 18 1 ; O1 C5
14 22 1 ; O1 C13
15 19 1 ; C2 C7
15 21 1 ; C2 C11
16 18 1 ; O3 C5
16 22 1 ; O3 C13
17 20 1 ; C4 C9
18 21 1 ; C5 C11
19 22 1 ; C7 C13
[ angles ]
;ai aj ak fu c0 c1
1 2 3 1 109.5 334.7 109.5 334.7 ; C1 O5 C6
2 3 4 1 120.0 418.4 120.0 418.4 ; O5 C6 O7
2 3 5 1 120.0 418.4 120.0 418.4 ; O5 C6 C8
4 3 5 1 121.0 502.1 121.0 502.1 ; O7 C6 C8
3 5 6 1 109.5 460.2 109.5 460.2 ; C6 C8 C10
3 5 13 1 109.5 460.2 109.5 460.2 ; C6 C8 C29
6 5 13 1 111.0 460.2 111.0 460.2 ; C10 C8 C29
5 6 7 1 109.5 460.2 109.5 460.2 ; C8 C10 N12
5 6 9 1 111.0 460.2 111.0 460.2 ; C8 C10 C18
7 6 9 1 104.0 460.2 104.0 460.2 ; N12 C10 C18
6 7 8 1 109.5 376.6 109.5 376.6 ; C10 N12 C14
6 7 11 1 104.0 460.2 104.0 460.2 ; C10 N12 C24
8 7 11 1 109.5 376.6 109.5 376.6 ; C14 N12 C24
6 9 10 1 104.0 460.2 104.0 460.2 ; C10 C18 C21
9 10 11 1 104.0 460.2 104.0 460.2 ; C18 C21 C24
7 11 10 1 104.0 460.2 104.0 460.2 ; N12 C24 C21
7 11 12 1 109.5 460.2 109.5 460.2 ; N12 C24 C26
10 11 12 1 109.5 460.2 109.5 460.2 ; C21 C24 C26
11 12 13 1 109.5 460.2 109.5 460.2 ; C24 C26 C29
5 13 12 1 109.5 251.0 109.5 251.0 ; C8 C29 C26
5 13 14 1 109.5 284.5 109.5 284.5 ; C8 C29 O1
12 13 14 1 109.5 284.5 109.5 284.5 ; C26 C29 O1
13 14 15 1 109.5 334.7 109.5 334.7 ; C29 O1 C2
14 15 16 1 120.0 418.4 120.0 418.4 ; O1 C2 O3
14 15 17 1 120.0 418.4 120.0 418.4 ; O1 C2 C4
16 15 17 1 121.0 502.1 121.0 502.1 ; O3 C2 C4
15 17 18 1 120.0 418.4 120.0 418.4 ; C2 C4 C5
15 17 22 1 120.0 418.4 120.0 418.4 ; C2 C4 C13
18 17 22 1 120.0 418.4 120.0 418.4 ; C5 C4 C13
17 18 19 1 120.0 418.4 120.0 418.4 ; C4 C5 C7
18 19 20 1 120.0 418.4 120.0 418.4 ; C5 C7 C9
19 20 21 1 120.0 418.4 120.0 418.4 ; C7 C9 C11
20 21 22 1 120.0 418.4 120.0 418.4 ; C9 C11 C13
17 22 21 1 120.0 418.4 120.0 418.4 ; C4 C13 C11
[ dihedrals ]
;ai aj ak al fu c0 c1 m c0 c1 m
3 2 5 4 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C6 O5
C8 O7
15 14 17 16 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C2 O1
C4 O3
17 22 18 15 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C4 C13
C5 C2
5 3 6 13 2 35.3 836.8 0 35.3 836.8 0 ; IDI C8 C6
C10 C29
6 5 7 9 2 35.3 836.8 0 35.3 836.8 0 ; IDI C10 C8
N12 C18
7 6 11 8 2 35.3 836.8 0 35.3 836.8 0 ; IDI N12 C10
C24 C14
11 7 12 10 2 35.3 836.8 0 35.3 836.8 0 ; IDI C24 N12
C26 C21
13 5 12 14 2 35.3 836.8 0 35.3 836.8 0 ; IDI C29 C8
C26 O1
17 18 19 20 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C4 C5
C7 C9
18 19 20 21 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C5 C7
C9 C11
19 20 21 22 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C7 C9
C11 C13
20 21 22 17 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C9 C11
C13 C4
21 22 17 18 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C11 C13
C4 C5
22 17 18 19 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C13 C4
C5 C7
1 2 3 5 1 180.0 16.7 2 180.0 16.7 2 ; DI C1 O5
C6 C8
13 5 3 2 1 0.0 0.4 6 0.0 0.4 6 ; DI C29 C8
C6 O5
9 6 5 3 1 0.0 5.9 3 0.0 5.9 3 ; DI C18 C10
C8 C6
3 5 13 14 1 0.0 5.9 3 0.0 5.9 3 ; DI C6 C8
C29 O1
5 6 7 11 1 0.0 3.8 3 0.0 3.8 3 ; DI C8 C10
N12 C24
10 9 6 5 1 0.0 5.9 3 0.0 5.9 3 ; DI C21 C18
C10 C8
12 11 7 6 1 0.0 3.8 3 0.0 3.8 3 ; DI C26 C24
N12 C10
11 10 9 6 1 0.0 5.9 3 0.0 5.9 3 ; DI C24 C21
C18 C10
9 10 11 12 1 0.0 5.9 3 0.0 5.9 3 ; DI C18 C21
C24 C26
13 12 11 7 1 0.0 5.9 3 0.0 5.9 3 ; DI C29 C26
C24 N12
14 13 12 11 1 0.0 5.9 3 0.0 5.9 3 ; DI O1 C29
C26 C24
5 13 14 15 1 0.0 3.8 3 0.0 3.8 3 ; DI C8 C29
O1 C2
13 14 15 17 1 180.0 16.7 2 180.0 16.7 2 ; DI C29 O1
C2 C4
22 17 15 14 1 180.0 5.9 2 180.0 5.9 2 ; DI C13 C4
C2 O1
On Wed, 2004-10-06 at 18:49, Yunfeng Hu wrote:
> In fact that is what I did. Here is what my topology file looks like:
> ;
> ; File '7a1.top' was generated
> ; By user: yunfenghu (501)
> ; On host: Yunfeng-Hus-Computer.local
> ; At date: Thu Sep 30 17:46:23 2004
> ;
> ; This is your topology file
> ; "Uh-oh .... Right Again" (Laurie Anderson)
> ;
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> #include "cocaine.itp"
Most likely your file cocaine.tip also includes a forcefield statement
and/or atomtypes and/or charges in cocaine.itp have to be adapted to
ffG43a1 (which are different than ffgmx).
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