[gmx-users] energy minimization of protein taken from PDB
jalemkul at vt.edu
Mon Nov 10 13:37:55 CET 2014
On 11/10/14 2:36 AM, md kashif wrote:
> Dear all
> I have downloaded a protein from RCSB, having two chains. In order to go
> for energy minimization should I delete one chain as both are similar and
> other molecules like SO4, water etc? Is the protein having chain A only can
> be used for energy minimization using tutorial
> I have gromacs 4.6.5 installed on my i7 processor laptop.
Whether or not you remove the second chain depends on whether or not it has any
functional significance or if it simply crystallizes as a dimer. For that, you
need to read the paper associated with the structure and make your decision.
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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