[gmx-users] Constraint of active site in gromacs

Justin Lemkul jalemkul at vt.edu
Wed May 6 13:43:42 CEST 2015

On 5/6/15 3:09 AM, Raj D wrote:
> Dear User,
> I would like to constraint the Iron bound active site of the protein in
> octahedral shape in EM and MD steps ... Is there a direct routine to create
> such a constraint in gromacs by feeding information of ligating atoms of
> amino acids with Iron at the center of the octahedral geometry.

What you need are distance restraints, which you will have to write in the 
topology yourself.



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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