[gmx-users] Peptide-membrane simulation force field parameters
tarak20489 at gmail.com
Sun Feb 15 13:44:05 CET 2015
Thanks Justin for the reply and suggestions.
I have more of less similar functional groups as that of the amino acid
Yes, I have figured out some chemical analogy to parametrize the residues.
On Wed, Feb 4, 2015 at 6:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
> 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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