[gmx-users] Fixing periodicity effects on trajectory file

Justin Lemkul jalemkul at vt.edu
Tue Sep 15 22:50:20 CEST 2015

On 9/15/15 1:24 PM, Homa rooz wrote:
> Dear Justin
> I have followed your advice but it didn't solve my problem.
> ​Ligand is still out of binding site.

Can you verify that it actually did start in the binding site?  Was everything 
built correctly?  If so, there's no reason that simply centering on the protein 
while putting the molecules in the box wouldn't work.  This is a single-chain 
protein, right?



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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