<br><br>Dear All,<br> When I try to grompp to generate .tpr file for mdrun from topology generated by prodrg I am getting the following error.<br><br>Generated 279 of the 1225 non-bonded parameter combinations<br>
Excluding 3 bonded neighbours molecule type 'PRODRG'<br><br>-------------------------------------------------------<br>Program grompp_d, VERSION 4.5.4<br>Source code file: toppush.c, line: 1987<br><br>Fatal error:<br>
No such moleculetype SOL<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>I am herewith attaching the chlor.top file please help me findout the problem.<br><br><br>;<br>; When using this software in a publication, cite:<br>; A. W. Schuettelkopf and D. M. F. van Aalten (2004).<br>
; PRODRG - a tool for high-throughput crystallography<br>; of protein-ligand complexes.<br>; Acta Crystallogr. D60, 1355--1363.<br>; <br>; <br><br>#include "ffG43a1.itp"<br><br>[ moleculetype ]<br>
; Name nrexcl<br>PRODRG 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 O 1 PDB OAE 1 -0.6772 15.9994 <br> 2 C 1 PDB CAK 1 0.8450 12.0110 <br>
3 C 1 PDB CAG 1 0.0134 12.0110 <br> 4 CL 1 PDB CLAA 1 -0.0968 35.4530 <br> 5 C 1 PDB CAH 2 0.0134 12.0110 <br> 6 CL 1 PDB CLAB 2 -0.0968 35.4530 <br>
7 C 1 PDB CAL 2 0.8450 12.0110 <br> 8 O 1 PDB OAF 2 -0.6772 15.9994 <br> 9 C 1 PDB CAJ 2 0.0134 12.0110 <br> 10 CL 1 PDB CLAD 2 -0.0968 35.4530 <br>
11 C 1 PDB CAI 2 0.0134 12.0110 <br> 12 CL 1 PDB CLAC 3 -0.0968 35.4530 <br><br>[ bonds ]<br>; ai aj fu c0, c1, ...<br> 2 1 2 0.123 16600000.0 0.123 16600000.0 ; CAK OAE <br>
2 3 2 0.139 10800000.0 0.139 10800000.0 ; CAK CAG <br> 2 11 2 0.139 10800000.0 0.139 10800000.0 ; CAK CAI <br> 3 4 2 0.173 2928800.0 0.173 2928800.0 ; CAG CLAA <br>
3 5 2 0.139 10800000.0 0.139 10800000.0 ; CAG CAH <br> 5 6 2 0.173 2928800.0 0.173 2928800.0 ; CAH CLAB <br> 5 7 2 0.139 10800000.0 0.139 10800000.0 ; CAH CAL <br>
7 8 2 0.123 16600000.0 0.123 16600000.0 ; CAL OAF <br> 7 9 2 0.139 10800000.0 0.139 10800000.0 ; CAL CAJ <br> 9 10 2 0.173 2928800.0 0.173 2928800.0 ; CAJ CLAD <br>
9 11 2 0.139 10800000.0 0.139 10800000.0 ; CAJ CAI <br> 11 12 2 0.173 2928800.0 0.173 2928800.0 ; CAI CLAC <br><br>[ pairs ]<br>; ai aj fu c0, c1, ...<br> 1 4 1 ; OAE CLAA <br>
1 5 1 ; OAE CAH <br> 1 9 1 ; OAE CAJ <br> 1 12 1 ; OAE CLAC <br>
2 6 1 ; CAK CLAB <br> 2 7 1 ; CAK CAL <br> 2 10 1 ; CAK CLAD <br>
3 8 1 ; CAG OAF <br> 3 9 1 ; CAG CAJ <br> 3 12 1 ; CAG CLAC <br>
4 6 1 ; CLAA CLAB <br> 4 7 1 ; CLAA CAL <br> 4 11 1 ; CLAA CAI <br>
5 10 1 ; CAH CLAD <br> 5 11 1 ; CAH CAI <br> 6 8 1 ; CLAB OAF <br>
6 9 1 ; CLAB CAJ <br> 7 12 1 ; CAL CLAC <br> 8 10 1 ; OAF CLAD <br>
8 11 1 ; OAF CAI <br> 10 12 1 ; CLAD CLAC <br><br>[ angles ]<br>; ai aj ak fu c0, c1, ...<br> 1 2 3 2 121.0 685.0 121.0 685.0 ; OAE CAK CAG <br>
1 2 11 2 121.0 685.0 121.0 685.0 ; OAE CAK CAI <br> 3 2 11 2 120.0 560.0 120.0 560.0 ; CAG CAK CAI <br> 2 3 4 2 120.0 560.0 120.0 560.0 ; CAK CAG CLAA <br>
2 3 5 2 120.0 560.0 120.0 560.0 ; CAK CAG CAH <br> 4 3 5 2 120.0 560.0 120.0 560.0 ; CLAA CAG CAH <br> 3 5 6 2 120.0 560.0 120.0 560.0 ; CAG CAH CLAB <br>
3 5 7 2 120.0 560.0 120.0 560.0 ; CAG CAH CAL <br> 6 5 7 2 120.0 560.0 120.0 560.0 ; CLAB CAH CAL <br> 5 7 8 2 121.0 685.0 121.0 685.0 ; CAH CAL OAF <br>
5 7 9 2 120.0 560.0 120.0 560.0 ; CAH CAL CAJ <br> 8 7 9 2 121.0 685.0 121.0 685.0 ; OAF CAL CAJ <br> 7 9 10 2 120.0 560.0 120.0 560.0 ; CAL CAJ CLAD <br>
7 9 11 2 120.0 560.0 120.0 560.0 ; CAL CAJ CAI <br> 10 9 11 2 120.0 560.0 120.0 560.0 ; CLAD CAJ CAI <br> 2 11 9 2 120.0 560.0 120.0 560.0 ; CAK CAI CAJ <br>
2 11 12 2 120.0 560.0 120.0 560.0 ; CAK CAI CLAC <br> 9 11 12 2 120.0 560.0 120.0 560.0 ; CAJ CAI CLAC <br><br>[ dihedrals ]<br>; ai aj ak al fu c0, c1, m, ...<br>
2 1 11 3 2 0.0 167.4 0.0 167.4 ; imp CAK OAE CAI CAG <br> 3 5 4 2 2 0.0 167.4 0.0 167.4 ; imp CAG CAH CLAA CAK <br> 5 7 6 3 2 0.0 167.4 0.0 167.4 ; imp CAH CAL CLAB CAG <br>
7 9 8 5 2 0.0 167.4 0.0 167.4 ; imp CAL CAJ OAF CAH <br> 9 11 10 7 2 0.0 167.4 0.0 167.4 ; imp CAJ CAI CLAD CAL <br> 11 12 9 2 2 0.0 167.4 0.0 167.4 ; imp CAI CLAC CAJ CAK <br>
2 3 5 7 2 0.0 209.3 0.0 209.3 ; imp CAK CAG CAH CAL <br> 3 5 7 9 2 0.0 209.3 0.0 209.3 ; imp CAG CAH CAL CAJ <br> 5 7 9 11 2 0.0 209.3 0.0 209.3 ; imp CAH CAL CAJ CAI <br>
7 9 11 2 2 0.0 209.3 0.0 209.3 ; imp CAL CAJ CAI CAK <br> 9 11 2 3 2 0.0 209.3 0.0 209.3 ; imp CAJ CAI CAK CAG <br> 11 2 3 5 2 0.0 209.3 0.0 209.3 ; imp CAI CAK CAG CAH <br>
<br>[ system ]<br>CHLORANIL BOX in water<br><br>[ molecules ]<br>PRODRG 1<br>SOL 17122<br><br>Thank you.<br>