AMBER Archive (2005)

Subject: Re: Re: AMBER: delphi and surface in MMPBSA

From: David A. Case (case_at_scripps.edu)
Date: Sat Oct 22 2005 - 11:44:37 CDT

On Fri, Oct 21, 2005, Yong Xu wrote:

> there are always different output for those two program using the same
> probe-radius.

I don't use MSMS myself. It would be interesting if someone could confirm
or deny this (molsurf vs. MSMS). In the past when I made comparisons, the
two gave the same results most of the time, and the differences were where
MSMS failed. But that was some time ago...

> what kind of surface are used for SA*0.00542 + 0.92 calculation by Molsurf
> in MMPBSA/AMBER?

You should use the SAS (solvent accessible surface) area here.

...dac

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