[gmx-users] including a new molecule to forcefield

Justin Lemkul jalemkul at vt.edu
Sun May 5 02:36:38 CEST 2013

On 5/4/13 8:34 PM, Amir Abbasi wrote:
> tnx but how can I make .top file?
> is there any tutorials?

Plenty.  Get yourself familiar with a "normal" Gromacs workflow before jumping 
in and doing something more complex.


> can I convert itp to top?

Sure.  They're hardly different.


Depending on what the contents of your system are, you may be almost 90% done 
with the topology you will need.


> 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


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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