[gmx-users] Simulating beta-peptides
jalemkul at vt.edu
Tue Jul 22 18:45:46 CEST 2014
On 7/22/14, 9:59 AM, Venkat Reddy wrote:
> Dear Gromacs users,
> Can I use GROMOS53A6 ff for simulating beta-peptides? I found some articles
> on beta peptide simulations using GROMOS53A6 and 53A7 ff. Do I have to edit
> any dihedral angle info to process my beta peptide after pdb2gmx step?
You'll have to write new force field files, the .rtp at minimum, because
beta-peptide connectivity is different. There may be new bonded parameters
involved, but those should be described in the literature.
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
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