[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides
jalemkul at vt.edu
Thu May 18 23:08:20 CEST 2017
On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote:
> I am trying to run simulations on alpha-D-glucose polymers. I have done these simulations using AMBER and I am wondering if it is possible to run them employing CHARMM36 in GROMACS, as well?
> It seams that CHARMM36 in GROMACS has only implemented monomers of alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the GROMACS?
Sure, you can treat it like any polymer, but you'll have to create the internal
monomer residues yourself from the patches in the original CHARMM force field files.
Or try CHARMM-GUI; it should handle what you need and give you all the necessary
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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