[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

Justin Lemkul jalemkul at vt.edu
Thu May 18 23:08:20 CEST 2017

On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote:
> Hi,
> 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 
GROMACS inputs.



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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