[gmx-users] Protein-Peptide Simulation help

Justin Lemkul jalemkul at vt.edu
Wed Dec 21 03:19:15 CET 2016

On 12/20/16 12:36 AM, Syed Azeem wrote:
> Hello All,
> I'm trying to simulate a Protein-Peptide complex using GROMACS 5.1.4.
> For reference, I referred Justin Lemkul's Tutorial for Protein Ligand
> complexes. In which, the topology for ligand (small molecule) was
> generated using PRODRG.
> In my case, do I need to treat my peptide (16-mer) in such a way? Or
> just directly simulating the protein-peptide complex is good enough?

A peptide is a protein.  Do not use PRODRG or any other such tools; just build 
its topology with pdb2gmx using the normal force field.



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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