[gmx-users] including a new molecule to forcefield

Amir Abbasi amir.abbasi69 at yahoo.com
Sun May 5 02:34:32 CEST 2013

tnx but how can I make .top file?
is there any tutorials?
can I convert itp to top?
or there is an other way?

 From: Justin Lemkul <jalemkul at vt.edu>
To: Amir Abbasi <amir.abbasi69 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, May 5, 2013 5:00 AM
Subject: Re: [gmx-users] including a new molecule to forcefield

On 5/4/13 8:28 PM, Amir Abbasi wrote:
> Hi All,
> I want to simulate graphene oxide in water. i have used swissparam server to create .itp file of it.
> then i'd put the .itp file in oplsaa.ff folder and edit forcefield.itp file and insert:
> #include "GRO.itp"

Do not edit forcefield.itp in this way.

> but when i want to use pdb2gmx to make topology file,it says:
> Residue 'GRO' not found in residue topology database
> what should i do?

Don't run pdb2gmx on the structure.  The job of pdb2gmx is to produce a 
topology, which you already have.  All you have to do is #include "GRO.itp" in 
your system's .top file.  Leave the other files in your force field folder alone.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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