AMBER Archive (2003)

Subject: Re: surface accesible area

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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_at_scripps.edu
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