[gmx-users] Constraint of active site in gromacs

Justin Lemkul jalemkul at vt.edu
Thu May 7 13:53:42 CEST 2015

On 5/7/15 6:33 AM, Raj D wrote:
> Dear Mark,
> So to make distance restrain of specific  atoms of  protein residues and
> the ligand (itp  file produced by antechamber), I may have to cut the
> ligating atoms of amino acids in the  topology as produced by pdb2gmx and
> paste into the ligand.itp to make the distance restraint to work ...Is it
> the right approach to bring all distance restrained atoms to bring into the
> same molecule type ?

You can't have a separate ligand topology for this to work.  It literally needs 
to be a merged [moleculetype] for everything that will participate in distance 
restraints.  That requires creation of an .rtp entry (not .itp file) for pdb2gmx 
to use in creating the topology, in concert with the -merge option.



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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