[gmx-users] Force Field for amino acid and peptide

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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