On Mon, Nov 20, 2000, Andreas Svrcek-Seiler wrote:
> is there a significant difference between
> imlicit solvent MD trajecories with and without the SA contribution ?
For already compact proteins or nucleic acids, the differences between
GB and GB/SA in structural terms is generally small, in our (limited)
experience. There have been reports from France of narrower minor grooves
in DNA when using GB/SA (compared to GB alone), but we have not been
able to reproduce that here.
For larger conformational changes (e.g. protein/peptide folding), one might
expect larger differences, although this has not yet been tested. But I
wish to re-emphasize that our experience with GB/SA is rather limited so
far.
...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 Tue Nov 21 2000 - 10:15:42 PST
