[gmx-users] energy minimization of protein taken from PDB

[Justin Lemkul]

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
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
http://mackerell.umaryland.edu/~jalemkul

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