[gmx-users] Peptide-membrane simulation force field parameters
jalemkul at vt.edu
Wed Feb 4 14:21:13 CET 2015
On 2/4/15 2:28 AM, tarak karmakar wrote:
> Dear All,
> I need a suggestion related to simulation of peptide-membrane system.
> Are CGenFF parameters (from ParamChem) for peptide analogues good enough to
> couple with Charmm36 parameters for the lipids in a membrane? (provided
> very low charge and param penalties)
The protein force field is highly optimized, and we generally recommend against
trying to shoehorn CGenFF parameters into it. Low penalties just indicate that
we cover the chemical space reasonably well in the force field, but that's not
necessarily an indicator that those parameters will properly represent a protein
moiety. What you have to remember about generalized force fields (CGenFF, GAFF,
etc) is that transferability comes at the expense of accuracy.
What kind of unnatural residue(s) do you have? Can it be parametrized by
analogy from existing functional groups without going to CGenFF? I would
recommend relying on the protein force field as much as possible. If you have
to derive anything via CGenFF, absolutely run the gamut of normal parameter
validation before relying on the parameters for production simulations.
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
More information about the gromacs.org_gmx-users