[gmx-users] energy minimization of protein taken from PDB
Justin Lemkul
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
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/index.html
> 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
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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