[gmx-users] Simulating protein peptide complex

Justin Lemkul jalemkul at vt.edu
Tue May 13 13:54:07 CEST 2014

On 5/13/14, 4:30 AM, Ruben Cloete wrote:
> Hi, Justin regarding protein peptide simulation do i prepare the peptide as i
> would a ligand (PRODRG) and add topology to .gro file?

No, just run it through pdb2gmx.

> Is there a tutorial for protein protein simulation?

No, because it's not really different from any other protein-in-water system.



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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