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

[Justin A. Lemkul]

Rini Gupta wrote:
> 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

You do not need to.

> I have to use different force field having already this entry (CS2)
> like ffgmx, ffgmx2 ?

The topology you wrote from PRODRG is for ffgmx.  This is a very outdated force 
field that the manual warns very clearly against using.

> It was wriiten on GROMACS website somewhere PRODRG server generate
> topologies compatible to ffgmx/GROMOS96 43A1

The original PRODRG creates ffgmx topologies.  PRODRG 2.5 (beta) can generate 
43A1 topologies, but neither is very trustworthy:

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

> 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
> 

These charges really make no sense.  Please refer to the paper linked above for 
the consequences of incorrect charges.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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