[gmx-users] Regarding mdrunfor small organic molecules
Ravi Kumar Venkatraman
ravikumarvenkatraman at gmail.com
Fri Aug 12 20:16:04 CEST 2011
Dear All,
When I try to grompp to generate .tpr file for mdrun from
topology generated by prodrg I am getting the following error.
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'PRODRG'
-------------------------------------------------------
Program grompp_d, VERSION 4.5.4
Source code file: toppush.c, line: 1987
Fatal error:
No such moleculetype SOL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I am herewith attaching the chlor.top file please help me findout the
problem.
;
; 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.
;
;
#include "ffG43a1.itp"
[ moleculetype ]
; Name nrexcl
PRODRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 O 1 PDB OAE 1 -0.6772 15.9994
2 C 1 PDB CAK 1 0.8450 12.0110
3 C 1 PDB CAG 1 0.0134 12.0110
4 CL 1 PDB CLAA 1 -0.0968 35.4530
5 C 1 PDB CAH 2 0.0134 12.0110
6 CL 1 PDB CLAB 2 -0.0968 35.4530
7 C 1 PDB CAL 2 0.8450 12.0110
8 O 1 PDB OAF 2 -0.6772 15.9994
9 C 1 PDB CAJ 2 0.0134 12.0110
10 CL 1 PDB CLAD 2 -0.0968 35.4530
11 C 1 PDB CAI 2 0.0134 12.0110
12 CL 1 PDB CLAC 3 -0.0968 35.4530
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.123 16600000.0 0.123 16600000.0 ; CAK OAE
2 3 2 0.139 10800000.0 0.139 10800000.0 ; CAK CAG
2 11 2 0.139 10800000.0 0.139 10800000.0 ; CAK CAI
3 4 2 0.173 2928800.0 0.173 2928800.0 ; CAG CLAA
3 5 2 0.139 10800000.0 0.139 10800000.0 ; CAG CAH
5 6 2 0.173 2928800.0 0.173 2928800.0 ; CAH CLAB
5 7 2 0.139 10800000.0 0.139 10800000.0 ; CAH CAL
7 8 2 0.123 16600000.0 0.123 16600000.0 ; CAL OAF
7 9 2 0.139 10800000.0 0.139 10800000.0 ; CAL CAJ
9 10 2 0.173 2928800.0 0.173 2928800.0 ; CAJ CLAD
9 11 2 0.139 10800000.0 0.139 10800000.0 ; CAJ CAI
11 12 2 0.173 2928800.0 0.173 2928800.0 ; CAI CLAC
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; OAE CLAA
1 5 1 ; OAE CAH
1 9 1 ; OAE CAJ
1 12 1 ; OAE CLAC
2 6 1 ; CAK CLAB
2 7 1 ; CAK CAL
2 10 1 ; CAK CLAD
3 8 1 ; CAG OAF
3 9 1 ; CAG CAJ
3 12 1 ; CAG CLAC
4 6 1 ; CLAA CLAB
4 7 1 ; CLAA CAL
4 11 1 ; CLAA CAI
5 10 1 ; CAH CLAD
5 11 1 ; CAH CAI
6 8 1 ; CLAB OAF
6 9 1 ; CLAB CAJ
7 12 1 ; CAL CLAC
8 10 1 ; OAF CLAD
8 11 1 ; OAF CAI
10 12 1 ; CLAD CLAC
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 121.0 685.0 121.0 685.0 ; OAE CAK
CAG
1 2 11 2 121.0 685.0 121.0 685.0 ; OAE CAK
CAI
3 2 11 2 120.0 560.0 120.0 560.0 ; CAG CAK
CAI
2 3 4 2 120.0 560.0 120.0 560.0 ; CAK CAG
CLAA
2 3 5 2 120.0 560.0 120.0 560.0 ; CAK CAG
CAH
4 3 5 2 120.0 560.0 120.0 560.0 ; CLAA CAG
CAH
3 5 6 2 120.0 560.0 120.0 560.0 ; CAG CAH
CLAB
3 5 7 2 120.0 560.0 120.0 560.0 ; CAG CAH
CAL
6 5 7 2 120.0 560.0 120.0 560.0 ; CLAB CAH
CAL
5 7 8 2 121.0 685.0 121.0 685.0 ; CAH CAL
OAF
5 7 9 2 120.0 560.0 120.0 560.0 ; CAH CAL
CAJ
8 7 9 2 121.0 685.0 121.0 685.0 ; OAF CAL
CAJ
7 9 10 2 120.0 560.0 120.0 560.0 ; CAL CAJ
CLAD
7 9 11 2 120.0 560.0 120.0 560.0 ; CAL CAJ
CAI
10 9 11 2 120.0 560.0 120.0 560.0 ; CLAD CAJ
CAI
2 11 9 2 120.0 560.0 120.0 560.0 ; CAK CAI
CAJ
2 11 12 2 120.0 560.0 120.0 560.0 ; CAK CAI
CLAC
9 11 12 2 120.0 560.0 120.0 560.0 ; CAJ CAI
CLAC
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 11 3 2 0.0 167.4 0.0 167.4 ; imp CAK OAE
CAI CAG
3 5 4 2 2 0.0 167.4 0.0 167.4 ; imp CAG CAH
CLAA CAK
5 7 6 3 2 0.0 167.4 0.0 167.4 ; imp CAH CAL
CLAB CAG
7 9 8 5 2 0.0 167.4 0.0 167.4 ; imp CAL CAJ
OAF CAH
9 11 10 7 2 0.0 167.4 0.0 167.4 ; imp CAJ CAI
CLAD CAL
11 12 9 2 2 0.0 167.4 0.0 167.4 ; imp CAI CLAC
CAJ CAK
2 3 5 7 2 0.0 209.3 0.0 209.3 ; imp CAK CAG
CAH CAL
3 5 7 9 2 0.0 209.3 0.0 209.3 ; imp CAG CAH
CAL CAJ
5 7 9 11 2 0.0 209.3 0.0 209.3 ; imp CAH CAL
CAJ CAI
7 9 11 2 2 0.0 209.3 0.0 209.3 ; imp CAL CAJ
CAI CAK
9 11 2 3 2 0.0 209.3 0.0 209.3 ; imp CAJ CAI
CAK CAG
11 2 3 5 2 0.0 209.3 0.0 209.3 ; imp CAI CAK
CAG CAH
[ system ]
CHLORANIL BOX in water
[ molecules ]
PRODRG 1
SOL 17122
Thank you.
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