[gmx-users] GROMPP COMMAND

[Justin Lemkul]

On 7/7/14, 12:49 AM, Andy Chao wrote:
> Dear GROMACS Users:
>
> I have a question regarding using the GROMPP command..
>
> I first used the g_x2top command to convert the *.gro file of a graphene
> sheet to the *.top file of the graphene sheet by using the forcefield.itp
> file in the OPLSAA file folder as the following:
>
> g_x2top -f graphene.gro -ff oplsaa -o graphene.top
>
> and then use the grompp to run energy minimization
>
> grompp -f em.mdp -c graphene.gro -p graphene.top -o NPT.ptr
>
> why do I get error messages as the following:
>
> Program grompp, Version 4.6.5
> source code file: /build/buildd/gromacs-4.6.5/src/kernel/topio.c, line: 752
>
> Fatal error:
> Syntax error - File forcefield.itp, line 24
> Last line read:
> 'opls_071  CG   6   12.01100   0.00   A 3.500000E-01   2.92880E-01'
> Found a second deaults directive.
>
> What I don't understand is, why the same forcefield.itp file that allows
> the *.gro file to be converted to the *.top file has problems when we try
> to use it to run the grompp file?
>
> How should I fix this problem?
>

Something is broken within graphene.top, but unless you post the file for 
download somewhere, there's nothing anyone can suggest.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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