AMBER Archive (2000)

Subject: Re: GB vs. GB/SA

From: David Case (case_at_scripps.edu)
Date: Tue Nov 21 2000 - 12:15:42 CST

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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