Re: polarizabitlity

From: David A. Case <>
Date: Mon 18 Nov 2002 16:44:10 -0800

On Fri, Nov 15, 2002, X. Tan wrote:
> I have some questions about polarizability. In amber manual, it said"
> charges are normally scaled when polarizability are used..." Is there
> anyone can explain this to me. Why need to do this?

This is somewhat out of date by now. One early and simple model for charges
to be used with a polarizable force field was to scale the effective charges
in a non-polarizable model by some constant factor. But it is probably no
longer "normal" to do things this way, and we will update the manual.

It is presumably better instead to use the polarizable version of RESP, in
which charges are fit to quantum-mechanically derived electrostatic
potentials. This is what has been done for the "ff02" and "ff02EP"
polarizable force fields in Amber. See:

%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

Note that for standard amino acids and nucleic acids, you don't have to "do"
anything: the charges you get with ff02 or ff02EP are those created by the
above procecdure. But you could use these ideas to extend these force fields
to other molecules (e.g. to ligands).

Of course, if you just want to build your own polarizable force field from
scratch, you are free to develop a charge model in any manner that pleases
you, and scaling of non-polarizable charges might be a good first guess.

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Mon Nov 18 2002 - 16:44:10 PST
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