Dear gmx users,<br />
<br />
I am using gromacs (version 4.0.7) first time <br />
to setup a 2-butoxyethanol-water simulation.<br />
I created topology and coordinate file for BE using PRODRG server. <br />
Then a generated a box containing 20 BE and 480 water molecules using <br />
genbox.<br />
<br />
Now, when I am trying to do energy minimization using ffG43a1 force <br />
field it is giving error message :<br />
<br />
-------------------------------------------------------------<br />
Program grompp_d_mpi, VERSION 4.0.7<br />
Source code file: toppush.c, line: 947<br />
<br />
Fatal error:<br />
Atomtype CS2 not found<br />
--------------------------------------------------------------<br />
<br />
While searching through gmx-users mailing list I understand that my <br />
force field I am using doesn't contain atom type CS2.<br />
My question is can I add this particular atom type to force field file <br />
I want to use.<br />
If so how? or<br />
I have to use different force field having already this entry (CS2) <br />
like ffgmx, ffgmx2 ?<br />
It was wriiten on GROMACS website somewhere PRODRG server generate <br />
topologies compatible to ffgmx/GROMOS96 43A1<br />
force fields. But energy minimization is completed only when I am using <br />
ffgmx force field.<br />
<br />
<br />
I am using following topology file:<br />
-----------------------------------------------------------------------<br />
--------------------<br />
; Include forcefield parameters<br />
#include "ffG43a1.itp"<br />
<br />
[ moleculetype ]<br />
; Name nrexcl<br />
DRG 3<br />
<br />
[ atoms ]<br />
; nr type resnr resid atom cgnr charge mass<br />
1 CH3 1 DRG CAA 1 -0.016 15.0350<br />
2 CH2 1 DRG CAB 1 0.016 14.0270<br />
3 CH2 1 DRG CAC 2 0.000 14.0270<br />
4 CS2 1 DRG CAD 3 0.140 14.0270<br />
5 OS 1 DRG OAE 3 -0.280 15.9994<br />
6 CS2 1 DRG CAF 3 0.140 14.0270<br />
7 CH2 1 DRG CAG 4 0.065 14.0270<br />
8 OA 1 DRG OAH 4 -0.094 15.9994<br />
9 HO 1 DRG HAA 4 0.029 1.0080<br />
<br />
[ bonds ]<br />
; ai aj fu c0, c1, ...<br />
1 2 1 0.153 334720.0 0.153 334720.0 ; CAA CAB<br />
2 3 1 0.153 334720.0 0.153 334720.0 ; CAB CAC<br />
3 4 1 0.153 334720.0 0.153 334720.0 ; CAC CAD<br />
4 5 1 0.144 251040.0 0.144 251040.0 ; CAD OAE<br />
5 6 1 0.144 251040.0 0.144 251040.0 ; OAE CAF<br />
6 7 1 0.153 334720.0 0.153 334720.0 ; CAF CAG<br />
7 8 1 0.143 334720.0 0.143 334720.0 ; CAG OAH<br />
8 9 1 0.100 313800.0 0.100 313800.0 ; OAH HAA<br />
<br />
[ pairs ]<br />
; ai aj fu c0, c1, ...<br />
1 4 1 ; CAA CAD<br />
2 5 1 ; CAB OAE<br />
3 6 1 ; CAC CAF<br />
4 7 1 ; CAD CAG<br />
5 8 1 ; OAE OAH<br />
6 9 1 ; CAF HAA<br />
<br />
[ angles ]<br />
; ai aj ak fu c0, c1, ...<br />
1 2 3 1 111.0 460.2 111.0 460.2 ; CAA CAB <br />
CAC<br />
2 3 4 1 111.0 460.2 111.0 460.2 ; CAB CAC <br />
CAD<br />
3 4 5 1 109.5 284.5 109.5 284.5 ; CAC CAD <br />
OAE<br />
4 5 6 1 109.5 334.7 109.5 334.7 ; CAD OAE <br />
CAF<br />
5 6 7 1 109.5 284.5 109.5 284.5 ; OAE CAF <br />
CAG<br />
6 7 8 1 109.5 460.2 109.5 460.2 ; CAF CAG <br />
OAH<br />
7 8 9 1 109.5 397.5 109.5 397.5 ; CAG OAH <br />
HAA<br />
<br />
[ dihedrals ]<br />
; ai aj ak al fu c0, c1, m, ...<br />
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD <br />
CAC CAB CAA<br />
2 3 4 5 1 0.0 5.9 3 0.0 5.9 3 ; dih CAB <br />
CAC CAD OAE<br />
3 4 5 6 1 0.0 3.8 3 0.0 3.8 3 ; dih CAC <br />
CAD OAE CAF<br />
7 6 5 4 1 0.0 3.8 3 0.0 3.8 3 ; dih CAG <br />
CAF OAE CAD<br />
5 6 7 8 1 0.0 5.9 3 0.0 5.9 3 ; dih OAE <br />
CAF CAG OAH<br />
6 7 8 9 1 0.0 1.3 3 0.0 1.3 3 ; dih CAF <br />
CAG OAH HAA<br />
<br />
; Include water topology<br />
#include "spce.itp"<br />
<br />
<br />
[ system ]<br />
; Name<br />
BE in Water<br />
<br />
[ molecules ]<br />
; Compound #mols<br />
DRG 20<br />
SOL 480<br />
-----------------------------------------------------------------------<br />
---------------------------------------<br />
<br />
<br />
<br />
<br />
Can someone please help me in this regard.<br />
<br />
<br />
Thanks and Regards,<br />
Rini<br />
<br />
-------------------------<br />
Dr. Rini Gupta<br />
Post doctoral Fellow<br />
Department of Chemistry<br />
University of British Columbia<br />
Vancouver<br />
<br />
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