[gmx-users] A quick question regarding topology generation

Justin Lemkul jalemkul at vt.edu
Fri Feb 6 22:31:22 CET 2015

On 2/6/15 3:37 PM, Agnivo Gosai wrote:
> Dear Users
> During topology generation many a times we clean the PDB file by stripping
> it off waters ( crystallized ) or some other small molecules ( like a small
> ligand ) etc , which are of no immediate interest , as we concentrate on
> getting the structure for the protein ( biomolecule ) upon which we want to
> perform molecular dynamics.
> My question is will that create any distortion on the protein structure
> generated by "pdb2gmx"? One of my colleagues told me that the other atoms
> like those of the water and the small ligands may be participating in
> hydrogen bonds with the protein which can stabilize the structure. So if I
> remove them then I am making the protein structure unstable. I told him
> that I do energy minimization after solvation to stabilize my structure but
> he is saying that it is unstable since the beginning.

If the crystal waters or ligands are structurally or functionally important, 
they can have an effect.  Waters on the surface of the protein probably don't 
matter at all (in most cases), but waters in the active/binding site may be 
significant, though if their removal causes some massive distortion in the 
structure, I'd be suspect about a lot more before I'd blame water.  Proper 
equilibration with restraints on the protein, allowing water to soak into 
available volume, will probably alleviate most issues you might encounter. 
Rushing the equilibration could negatively impact the outcome.  Ligand binding 
can induce significant conformational change.



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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