[gmx-users] topology file

[Justin Lemkul]

On 6/25/14, 12:52 AM, Andy Chao wrote:
> Hi,
>
> I have a few technical questions regarding creating the topology file by
> using the command "g_x2top".
>
> I would like to use the following GROMACS's command:
>
> g_x2top -f device.gro -ff oplsaa -o device.top
>
> to convert the .gro file to .top.
>
> The problem that I have is that the force field for carbon (graphene sheet)
> and C4mimNTf2 are not defined.  Would you please let me know which file
> must be modified in order to define the force field for carbon and the
> elements in C4mimNTf2?
>

ffnonbonded.itp is where you can specify nonbonded parameters for new atom types.

-Justin

-- 
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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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