[gmx-users] virtual sites

Justin Lemkul jalemkul at vt.edu
Tue Oct 29 13:04:49 CET 2013

On 10/29/13 2:21 AM, Neha Gandhi wrote:
> Dear Users,
> I have a system consisting of peptides and a linear carbohydrate.
> Initially I tried to simulate these peptides using virtual sites and
> it worked. I can use pdb2gmx for building virtual sites on protein
> whereas I have an itp file for the carbohydrate. Is it possible to
> apply virtual site to a carbohydrate along with the peptides?

Sure, have you tried?  Were there problems?



Justin A. Lemkul, Ph.D.
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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