[gmx-users] Defining +/- in the RTP file for a molecule with 3 different molecules

Justin Lemkul jalemkul at vt.edu
Wed Dec 7 17:17:38 CET 2016

On 12/7/16 11:06 AM, Aishwary Shivgan wrote:
> Hello everyone,
> Generally the +/- works for bonds, angles, dihedral for the molecules
> connected linearly but Is there a way to define the +/- connections of a
> new residue which is connected by 3 different residues.

pdb2gmx can only create linear connections via .rtp entries, but can create 
branch points via entries in specbond.dat.



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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