On Wed, Jan 29, 2003, Arvid Soederhaell wrote:
>
> I would like to start using antechamber but it looks like it needs
> gaussian output for proper assignment of resp charges. Is this correct?
> Previously I have used gamess for generation of a ESP input to the RESP
> program. Can't I use that for antechamber?
The "automatic" part of antechamber currently requires Gaussian. But
you can continue to use GAMESS as you have in the past, and insert the
charges manually into your prepi or mol2 files.
>
> What is the general oppinion about using, for example Gasteiger charges
> instead of resp charges? Isn't resp considered to be the best in
> combination with amber f.f.?
>
The GAFF force field was designed to be compatible with the Amber protein/
nucleic acid force field, and best results are obtained with RESP charges.
A reasonable alternative is to use AM1/BCC charges, which were designed to
mimic RESP charges, but starting from a much cheaper wavefunction. We have
definitely seen worse results (e.g. poor solvation free energies) when using
Gasteiger charges.
..hope this helps...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
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Received on Wed Jan 29 2003 - 08:16:03 PST
