[gmx-users] Defining +/- in the RTP file for a molecule with 3 different molecules
aishwary55 at gmail.com
Thu Dec 8 08:31:26 CET 2016
Thanks for the reply.
I will try to implement specbond in my system. Just want to ask if it could
be implemented for the following molecule having multiple branch points in
a single molecule?
Ultimately I want to attach the glycan to the protein.
On Thu, Dec 8, 2016 at 2:26 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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.
> 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
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