[gmx-users] Protein Drug simulation Parameters

Justin Lemkul jalemkul at vt.edu
Mon Sep 26 14:11:19 CEST 2016

On 9/26/16 4:43 AM, tasneem kausar wrote:
> Dear All
> I have performed MD simulation of protein and drug crystal structure. I
> have generated drug  itp file from PRODRG server and corrected the charges
> of atoms as suggested in Justin's paper J. Chem. Inf. Model. 2010, 50,
> 2221–2235.
> I have done 50 ns MD simulation of protein and drug using g43a1 force field
> and spc water model. After 15 ns drug molecule comes out of the pocket.
> Is this expected during MD simulation. If this occurs what is the reason
> behind it.
> Should we change any specific parameter for protein drug simulation.

First, make sure it is not a simple periodicity issue by re-imaging the 
trajectory with trjconv.  Several iterations will likely be necessary; see 

If there is some legitimate problem that leads to ligand dissociation, either 
your run settings are inappropriate, the initial geometry has large clashes that 
lead to large forces that expel the ligand, or the ligand topology is incorrect 
and overly attracted to the bulk aqueous environment.



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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