From: David A. Case <>
Date: Mon, 17 Oct 2005 08:10:17 -0700

On Wed, Oct 12, 2005, Yong Xu wrote:
> I want to do some MMPBSA work on a series of small molecules composed of F,
> Cl, Br, or I atoms. but there are no parameter for those elements.

These atoms have not been parameterized in the Amber scheme (as far as I
know), but the "Bondi" radii should give good starting points:

%A A. Bondi
%J J. Chem. Phys.
%V 64
%P 441
%D 1964

Maybe some list-members who have done large scale calculations can pitch in
with ideas. Note that the only thing "missing" are parameters for the surface
area part (please let me know if I am wrong here), and I don't think that
small uncertainties in the parameters for halogens would lead to much overall
uncertainty in the final results: getting good charges (and therefore good C-X
bond dipoles) is probably much more important.

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Received on Mon Oct 17 2005 - 16:53:00 PDT
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