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

Justin Lemkul jalemkul at vt.edu
Wed Dec 7 19:27:10 CET 2016

On 12/7/16 11:58 AM, Aishwary Shivgan wrote:
> Hello everyone,
> Thank you Justin, for the reply.
> My system is a complex glycan and has many such branch points. Attached the
> picture of the one I am working on.
> I am looking at the contents of the specbond.dat
> Could you help me understand how this works for one of the lines in the
> specbond.dat
> CYS     SG      1       HEM     CAB     1       0.18    CYS2    HEME
> Another option would be to write the rtp for the whole molecule but that
> would become very big. What I am aiming for is to define different sugars
> as different residues so that I can build any type of the glycan from
> available sugars in rtp file.

Please read manual section 5.7.7.



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


More information about the gromacs.org_gmx-users mailing list