[gmx-users] fatal error trying to simulate glycosylated proteins

Justin Lemkul jalemkul at vt.edu
Mon Feb 15 02:22:50 CET 2016

On 2/14/16 8:19 PM, David Newman wrote:
> Hi,
> I'm trying to simulate the dynamics of glycosylated proteins using gromacs 4.6.5 and have acquired forcefield parameters from PTM-Vienna (ffG45a3(v1.6) and ffG54a7(v1.7)) and CHARMM-GUI (36-jun2015) that supposedly allow for analysis of PTMs but both result in a fatal error when trying to run pdb2gmx -failing to recognise the identifier NAG - is there an alternative identifier I can use?

I can't speak to the GROMOS parameter sets, but the CHARMM-GUI output should 
include everything you need - force field, topology, coordinates, and .mdp files 
so there is no need to run pdb2gmx (because it won't handle glycosylations 
nicely and residue names may mismatch or not exist).



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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