[gmx-users] How to include specific atom in force field ffG43a1

[Rini Gupta]

Dear gmx users,

                        I am using gromacs (version 4.0.7)  first time 
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file for BE using PRODRG server. 
Then a generated a box containing 20 BE and 480 water molecules using 
genbox.

Now, when I am trying to do energy minimization  using ffG43a1 force 
field it is giving error message :

-------------------------------------------------------------
Program grompp_d_mpi, VERSION 4.0.7
Source code file: toppush.c, line: 947

Fatal error:
Atomtype CS2 not found
--------------------------------------------------------------

While searching through gmx-users mailing list I understand that my 
force field I am using doesn't contain atom type CS2.
My question is can I add this particular atom type to force field file 
I want to use.
If so how? or
I have to use different force field having already this entry (CS2) 
like ffgmx, ffgmx2 ?
It was wriiten on GROMACS website somewhere PRODRG server generate 
topologies compatible to ffgmx/GROMOS96 43A1
force fields. But energy minimization is completed only when I am using 
ffgmx force field.


I am using following topology file:
-----------------------------------------------------------------------
--------------------
; Include forcefield parameters
#include "ffG43a1.itp"

[ moleculetype ]
; Name nrexcl
DRG      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  DRG     CAA     1   -0.016  15.0350
     2       CH2     1  DRG     CAB     1    0.016  14.0270
     3       CH2     1  DRG     CAC     2    0.000  14.0270
     4       CS2     1  DRG     CAD     3    0.140  14.0270
     5        OS     1  DRG     OAE     3   -0.280  15.9994
     6       CS2     1  DRG     CAF     3    0.140  14.0270
     7       CH2     1  DRG     CAG     4    0.065  14.0270
     8        OA     1  DRG     OAH     4   -0.094  15.9994
     9        HO     1  DRG     HAA     4    0.029   1.0080

[ bonds ]
; ai  aj  fu    c0, c1, ...
   1   2   1    0.153    334720.0    0.153    334720.0 ;   CAA  CAB
   2   3   1    0.153    334720.0    0.153    334720.0 ;   CAB  CAC
   3   4   1    0.153    334720.0    0.153    334720.0 ;   CAC  CAD
   4   5   1    0.144    251040.0    0.144    251040.0 ;   CAD  OAE
   5   6   1    0.144    251040.0    0.144    251040.0 ;   OAE  CAF
   6   7   1    0.153    334720.0    0.153    334720.0 ;   CAF  CAG
   7   8   1    0.143    334720.0    0.143    334720.0 ;   CAG  OAH
   8   9   1    0.100    313800.0    0.100    313800.0 ;   OAH  HAA

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   4   1                                           ;   CAA  CAD
   2   5   1                                           ;   CAB  OAE
   3   6   1                                           ;   CAC  CAF
   4   7   1                                           ;   CAD  CAG
   5   8   1                                           ;   OAE  OAH
   6   9   1                                           ;   CAF  HAA

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   1    111.0       460.2    111.0       460.2 ;   CAA  CAB  
CAC
   2   3   4   1    111.0       460.2    111.0       460.2 ;   CAB  CAC  
CAD
   3   4   5   1    109.5       284.5    109.5       284.5 ;   CAC  CAD  
OAE
   4   5   6   1    109.5       334.7    109.5       334.7 ;   CAD  OAE  
CAF
   5   6   7   1    109.5       284.5    109.5       284.5 ;   OAE  CAF  
CAG
   6   7   8   1    109.5       460.2    109.5       460.2 ;   CAF  CAG  
OAH
   7   8   9   1    109.5       397.5    109.5       397.5 ;   CAG  OAH  
HAA

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
   4   3   2   1   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAD  
CAC  CAB  CAA
   2   3   4   5   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAB  
CAC  CAD  OAE
   3   4   5   6   1      0.0    3.8 3      0.0    3.8 3 ; dih   CAC  
CAD  OAE  CAF
   7   6   5   4   1      0.0    3.8 3      0.0    3.8 3 ; dih   CAG  
CAF  OAE  CAD
   5   6   7   8   1      0.0    5.9 3      0.0    5.9 3 ; dih   OAE  
CAF  CAG  OAH
   6   7   8   9   1      0.0    1.3 3      0.0    1.3 3 ; dih   CAF  
CAG  OAH  HAA

   ; Include water topology
#include "spce.itp"


[ system ]
; Name
BE in Water

[ molecules ]
; Compound      #mols
DRG               20
SOL               480
-----------------------------------------------------------------------
---------------------------------------




Can someone please help me in this regard.


Thanks and Regards,
Rini

-------------------------
Dr. Rini Gupta
Post doctoral Fellow
Department of Chemistry
University of British Columbia
Vancouver

  
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