[gmx-users] position restraints for different protein atoms
jalemkul at vt.edu
Sun Feb 21 21:26:41 CET 2016
On 2/20/16 11:16 PM, Irem Altan wrote:
> Is there a way to generate position restraint files such that the main chain
> atoms and the side chain atoms have different force constants? Similarly,
Yes, you can invoke genrestr with a suitable index group for whatever part of
the protein you want to set up with a given force constant.
> would it be possible to constrain atoms with B-factors lower than a certain
Only if you devise a way to parse such information. That probably involves
writing your own script to parse the B-factors in a PDB file and write those
atom numbers to an index file, which can then be fed to genrestr as stated above.
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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