Zlenko Dmitry wrote:
Well, I have a lipid bilayer whith unusual composition and unusual
lipids (whith irregular head groups). It's possible to calculate a
strength constant as second partial derivatives of full energy by
an apropriate coordinates (accordig, for example, to GAMES or PC
GAMES software). But, as I read, there are another more accurate
way, based on minimisation of disagriments between mechanical
potential energy surface and QM one:
this is beyond the capabilities of ffscan. you'll have to check
literature on parameterization for your favorite force field.
AFMM: A molecular mechanics force field vibrational
parametrization program. A.C. Vaiana 1, Z. Cournia, I.B. Costescu,
J.C. Smith. C.P.C. 167,34-42 (2005).
A quantum mechanical polarizable force field for biomolecular
interactions. A.G.Donchev, V.D.Ozrin, M.V.Subbotin, O.V.Tarasov,
and V.I.Tarasov. PNAS 102,7829-34 (2005);
Derivation of force fields for molecular mechanics and dynamics
from ab initio energy surfaces. J.R.Maple, U.Dinur, and
A.T.Hagler. Proc. Nati. Acad. Sci. 85,5350-54 (1988).
So, could ffscan help me or not?
Thank you for your attention,
Zlenko Dmitry.
Biophysical subdivisoin of
Biological faculty of Moscow State University.
Moscow, Russia.
[EMAIL PROTECTED]
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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