[gmx-users] Building topologies manually

Justin Lemkul jalemkul at vt.edu
Thu May 28 14:00:18 CEST 2015

On 5/27/15 10:00 PM, Vy Phan wrote:
> Dear Justin,
> I am so thankful for your reply.
> I still do not know how I can build the topology for the [image: $\gamma$]
> -Glu.
> I want to use gromos force field 54a7. Could you give some more guideline?

Instead of being at the alpha position, the peptide bond is formed via the 
sidechain gamma position.  The easiest route is to define a single .rtp that 
defines the tripeptide in its entirety.  Use existing building blocks and 
termini databases to get the correct charges and types on the Glu alpha amine 
and carboxylate.



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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