[gmx-users] GROMPP COMMAND

abhijit Kayal abhijitchemiitd at gmail.com
Mon Jul 7 07:34:45 CEST 2014

Can you tell how you make your topology file for graphene sheet?
Because normal way is to do that,
 first copy the oplsaa.ff file in your working directory, the make the
necessary changes in ffnonbonded.itp file and atomname2type.n2t files.
Then run g_x2top. The should not give any error.

On Mon, Jul 7, 2014 at 10:19 AM, Andy Chao <achao at energiaq.com> 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?
> Thanks!
> Andy
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Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur

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