[gmx-users] Defining +/- in the RTP file for a molecule with 3 different molecules
aishwary55 at gmail.com
Wed Dec 7 17:59:01 CET 2016
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
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.
On Thu, Dec 8, 2016 at 12:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users