[gmx-users] Fixing periodicity effects on trajectory file

Justin Lemkul jalemkul at vt.edu
Wed Sep 16 13:55:59 CEST 2015

On 9/16/15 1:23 AM, Homa rooz wrote:
> Dear Justin
> ​If you asked about verifying docking process​. I should say, I have worked
> with single chain protein and the best ranked binding energy was -7.41
> kcal/mol by AutoDock 4.2, considering that binding site was located on turn
> structure and the edge of protein, seeming unstable. I didn't check the
> result by another software.

Then what Michael said is likely true: your ligand dissociated and what you are 
observing is a real effect and not simply a PBC artifact.



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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