[gmx-users] position restraints for different protein atoms

Justin Lemkul jalemkul at vt.edu
Sun Feb 21 21:26:41 CET 2016

On 2/20/16 11:16 PM, Irem Altan wrote:
> Hi,
> 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
> threshold?

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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