[gmx-users] Force Field for amino acid and peptide
jalemkul at vt.edu
Thu May 26 03:03:16 CEST 2016
On 5/25/16 11:05 AM, Alexander Alexander wrote:
> Dear Gromacs user,
> I am going to simulate the binding free energy of some amino acid to a
> metal surface in aqueous solution and also peptide adsorption behavior into
> this surface.
> I know the force field of the surface as well as the better type of water
> for such a work, but I do not know which type of Force Filed could be the
> better choice for the peptide (amino acids) for this simulation, so I would
> be so appreciated if anybody could address me to a better choice of peptide
> (amino acid) Force Filed for such a goal?
One that is compatible with the force field of the surface. A force field is a
self-consistent entity. In general, you can't mix and match different parameter
sets from different sources, unless those parameter sets have a common origin or
shared method of parametrization. So your choice here for treatment of the
protein really isn't a free one, it's not about being the "better choice" for
the system; there can be only one answer, if it exists. Maybe there is no
protein force field compatible with whatever the surface is.
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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