Re: surface accesible area

From: David A. Case <case.scripps.edu>
Date: Fri, 7 Mar 2003 16:11:02 -0800

On Fri, Mar 07, 2003, Yongmei Wang wrote:
>
> Can I use AMBER to determine the surface accessible areas of a protein?

Amber uses the "LCPO" approximation developed by the Still group to estimate
these areas (see the Users' Manual). All you need to do is set gbsa=1.

The molsurf program (in src/mm_pbsa) can be used to obtain more accurate
estimates (at greater costs). This is most easily done using the mm_pbsa
scripts.

...dac 

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David A. Case                     |  e-mail:      case.scripps.edu
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Received on Sat Mar 08 2003 - 00:53:02 PST
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