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

Justin Lemkul jalemkul at vt.edu
Thu Dec 8 16:35:52 CET 2016

On 12/8/16 2:31 AM, Aishwary Shivgan wrote:
> 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?
> http://www.sigmaaldrich.com/content/dam/sigma-aldrich/
> life-science/biochemicals/migrationbiochemicals1/
> complex-tetraantennary-glyc.jpg
> Ultimately I want to attach the glycan to the protein.

You can probably get it to work, but it will be painful.  This is the sort of 
thing that GROMACS is admittedly not very good at doing, at least not easily.

Try http://www.charmm-gui.org/?doc=input/glycan instead.  It's designed to deal 
with complex glycosylation.  I can't remember if conversion to GROMACS format is 
included in the Glycan Reader yet, but if not, converting the topology shouldn't 
be that bad.



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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