[gmx-users] Clayff forcefield
jalemkul at vt.edu
Wed Aug 2 19:05:25 CEST 2017
On 8/2/17 5:20 AM, G R wrote:
> I try to implement CLYFF in gromacs. I created ffbonded.itp,
> ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and
> molecule.rtp. I want to simulate Kaolinite, and I try to use pdb2gmx to
> create a topology. My first question is that should I create any other
> files? second, In molecule.rtp, I just write the atom type, atom name
> charges. should I add bonds for each atom? Also, in rtp file, I don't
> what should I write as a residue?
For a system like you're dealing with, pdb2gmx is not the correct approach. Try
x2top with a suitable .n2t file (which you'll have to create).
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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