AMBER Archive (2005)

Subject: Re: AMBER: F,Cl,Br,I in MMPBSA

From: David A. Case (case_at_scripps.edu)
Date: Mon Oct 17 2005 - 10:10:17 CDT

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.

...dac
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