On Mon, Mar 11, 2002, Vojta Klusak wrote:
> When one wants to use polarisation in amber6, than he has to scale the
> charges (comand ScaleCharges in leap). What is the reason for doing that.
> Has it some physical meaning? Are the resp charges wrong? or is it simply
> fitting of the results at what we want to get?
Try looking at the following:
%A J.W. Caldwell
%A P.A. Kollman
%T Structure and properties of neat liquids using nonadditive molecular
dynamics: Water, methanol and N-methylacetaide
%J J. Phys. Chem.
%V 99
%P 6208-6219
%D 1995
%A P. Cieplak
%A J. Caldwell
%A P. Kollman
%T Molecular Mechanical Models for Organic and Biological Systems Going
Beyond the Atom Centered Two Body Additive Approximation: Aqueous Solution
Free Energies of Methanol and N-Methyl Acetamide, Nucleic Acid Base, and
Amide Hydrogen Bonding and Chloroform/Water Partition Coefficients of the
Nucleic Acid Bases
%J J. Computat. Chem.
%V 22
%P 1048-1057
%D 2001
Briefly, fixed charges represent on average the polarization from the
environment, and hence bond dipoles are typically "over-polarized" compared
to a gas-phase model. Adding in polarizabilties allows the fixed charges to
be smaller, since the polarizable dipoles take care of (part of) the
polarization.
...good luck...dac
(p.s. force field charges explicitly created for polarizable potentials (to
fit QM-calculated electrostatic potentials) are in the "ff02" force fields
in Amber 7.)
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Mon Mar 11 2002 - 09:37:51 PST
