[gmx-users] constrained bonds
jalemkul at vt.edu
Wed Dec 3 00:23:01 CET 2014
On 12/2/14 1:19 PM, marzieh dehghan wrote:
> Hi every body
> I created covalent bond by the latest version of autodock.according to the
> tutorial of protein-ligand complex with gromacs, the result of covalent
> bond was used for MD. after energy minimization, ligand was separated from
> I would like to know how can I occur constrained bond between protein and
> ligand to keep them in the suitable distance?
If you need an actual bond, as in the case of a covalently bound ligand, this is
a somewhat different case from most tutorials, which deal with the trivial case
of noncovalent binding. In the case of a covalently bound ligand, you need to
introduce a new residue into the force field.
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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