Thanks for the Dr. Case and Dr. Cieplak's kind response. I read that
paper, but I am still not sure how to get the correct charge for my
ligands.
So first I need optimize my molecules at HF/6-31G* level, then calculate
ESP using B3LYP/cc-pVTZ method, finally I can do RESP step. So could you
tell me which one is ESP(QM), and which one is ESP(ind)? Is there an
example for this kind of charge calculation?
Many thanks!
Xiaojian
On Mon, 18 Nov 2002, David A. Case wrote:
> 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 This is somewhat out of date by now.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: 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
> ==================================================================
>
>
Received on Tue Nov 19 2002 - 10:08:31 PST
