AMBER Archive (2004)

Subject: Re: AMBER: The question about SAS calculation in MM_PBSA

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 22 2004 - 13:29:52 CDT

On Mon, Sep 20, 2004, Jack Lei wrote:
>
> Now we know MSMS is good in surface calculation. In MM_PBSA,
> AMBER used MOLSURF to calculate SAS surface area. I am just
> curious that anybody tried this using MSMS instead of MOLSURF.

The problem with MSMS is that it will sometimes fail to give the correct
surface area, missing some parts of the surface because of the iterative way
in which the calculation is carried out. Hence, given a few hundred very
similar protein snapshots, MSMS may fail on a small number, which complicates
the data analysis. This, plus the fact that the source code for MSMS is not
generally available, led us to use MOLSURF instead.

...dac

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