Re: [AMBER] Molsurf: some questions on usage

From: David A Case <>
Date: Fri, 28 Aug 2015 08:03:18 -0400

On Thu, Aug 27, 2015, George Tzotzos wrote:

> I’m trying to calculate the Connolly SASA of a ligand in the free and
> bound state.
> From literature, I obtained some reference values which I quote "The
> solvent accessible surface area of the ligand is reduced from 388 A^2 in
> the free state to 38 A^2 in the bound state”.
> The results obtained using molsurf are way out. I obtained 220 A^2.

These are indeed quite different. Did you add 1.4 Ang to all the input radii,
then use a probe radius of zero? Have you checked what radii were used in the
"literature" value?

You can obtain the original "ms" program from a variety of sources (including
the SHIFTS package at, compare
values. Michel Sanner's "msms" program is also available from many sites, and
can be used for comparison. But I don't know of any problems with molsurf
(other than when it prints out warnings of its own limitations.)


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Received on Fri Aug 28 2015 - 05:30:03 PDT
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