[gmx-users] Protein preparation

Justin Lemkul jalemkul at vt.edu
Sun Mar 26 22:17:27 CEST 2017

On 3/26/17 12:39 PM, Quin K wrote:
> Thank you for the reply.
> I have another question. I used MODELLER on Chimera to fix the protein and
> found that there were significant visible changes to structure of protein.
> I'm not sure whether to use the old protein or the fixed one.
> Does it really matter that I used unfixed protein if the structure of
> binding site(s) and important chain features remain the same ?
> For the 50 ns MD simulation I never fixed the protein.

This all depends on what "fixed" means.  Were there missing residues?  Clashes 
in the structure?  In the case of the former, without a "fix" then the missing 
residues will cause lots of problems.  In the case of the latter, energy 
minimization is usually sufficient to alleviate any problems.



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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