AMBER Archive (2006)

Subject: Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ????

From: David A. Case (case_at_scripps.edu)
Date: Sat Jun 10 2006 - 13:24:29 CDT

On Sat, Jun 10, 2006, linfu wrote:

>
> In MMPBSA, SAS is calculated by Molsurf.(1.4 A probe)

I don't think this is correct. According to the manual, the probe radius
should be set to zero, which is required to get an SAS from the molsurf
program. See the comments and instructions in the "MS" section of the
mm-pbsa chapter in the users manual (p. 292 for Amber 9).

As Ray Luo suggested, you will have to be more specific about what radii and
parameters you used, both for mm-pbsa and for the sybyl/MSMS calculation.
Note also that you can run molsurf "by hand" (outside the mm-pbsa script)
to experiment about what results it is giving.

...good luck...dac

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