[gmx-users] protein-ligand complex

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Fri Jan 17 15:57:54 CET 2014

dear justin 
thanks a lot
if i use flexible receptor in docking process, must i  change  the coordinates of the protein as initial configuration  in the MD simulation?

On Friday, January 17, 2014 4:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 1/17/14, 3:15 AM, Mahboobeh Eslami wrote:
> dear justin
> i have another question
> Can the increasing of  MD simulation time improve docking results?  can the
> increasing of  MD simulation time create the experimental conformation of the
> ligand in the active site of the protein or close to it?

Possibly, but the original point stands - if the initial pose is very poor or 
the topology incorrect, more running time usually just means more wasted time. 
You need to establish whether or not your starting conditions are reasonable.



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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