[gmx-users] Element naming format in .pdb file

Justin Lemkul jalemkul at vt.edu
Sat Dec 20 15:14:58 CET 2014

On 12/20/14 12:12 AM, Rajan Kumar wrote:
> Dear all,
> I am trying to study wetting of Graphene oxide. I have prepared a structure
> file using material studio, which I will simulate in GROMACS.
> My structure contain some epoxy and hydroxyl functional group in Graphene
> sheet. However, the structure file generated does not differentiate between
> carbon atoms with and without functional group in the "Name" column of .pdb
> file. Also there is no differentiation in naming format of oxygen atom in
> epoxy and hydroxyl group.
> Since, these atoms will have different atom type in atomtype.atp file of
> force filed.(I will be using OPLS-AA for simulation). Do I have to make
> edits in .pdb file for different atomtypes as well.

To prepare the topology for this system, you need g_x2top, whose input is an 
.n2t file that allows you to specify atom types based on connectivity.  This 
should work fine for what you need to do.  Do not use pdb2gmx; it will not work.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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