[gmx-users] retaining the active site water molecules in the protein -reg

Justin Lemkul jalemkul at vt.edu
Wed Oct 15 13:39:13 CEST 2014

On 10/15/14 5:06 AM, venkatesh s wrote:
> hello
> In my task some water molecules in one protein active site and it playing
> one of the role of interactions and binding affinity
> if i want retain that water molecules in active site  to preform the
> simulations what i want to do ? further

Simply retain the coordinates in the starting structure when running pdb2gmx. 
Note that pdb2gmx will generate some spurious bond and angle interactions in the 
case of rigid water, so either (1) remove those interactions in the topology 
afterwards or (2) separate the protein and water, process the protein, and 
simply paste back the water coordinates and proceed.



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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