AMBER Archive (2003)

Subject: Re: AMBER: MSMS

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 23 2003 - 12:56:32 CST

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_at_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 

-- 

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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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