On Tue, Dec 23, 2003, Salma B. Rafi wrote:
>
> I am trying to use MSMS to calculate the solvent accessible surface area
> of a BIG protein. In the output, there are numbers corresponding to
> reent, toric, contact, SES and SAS. I would like to know which term
> refers to the solvent accessible surface area :"Contact" or the "SAS"???
First, questions about MSMS should really be directed to its author, Michel
Sanner, <sanner.scripps.edu>; msms is not part of the amber suite. Michel's
web page may help: http://www.scripps.edu/~sanner/.
Second, be sure you understand the various types of "surface area" one might
be interested in. "SAS" stands for solvent-accessible surface", and its
area is probably what you want. But this is different than the area of the
so-called "molecular" (or "Connolly") surface.
...hope this helps...dac
--
==================================================================
David A. Case | e-mail: case.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 14 2004 - 15:53:12 PST
