[gmx-users] g_sas, what's it all about?

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 31 16:28:24 CEST 2008

Michel Cuendet wrote:
> Hi list,
> I wanted to post something about g_sas some time ago already, but didn't 
> find time to. Here is the occasion.
> I believe g_sas does not actually compute the solvent accessible surface 
> area (SASA, defined as the locus of the center of the probe sphere), but 
> rather the molecular surface (defined using the surface of the probe 
> sphere). See
> http://www.netsci.org/Science/Compchem/feature14e.html
> This should really be explained in the help of g_sas, together with the 
> references for the algorithm used. It would also be nice to have an 
> option to calculate the true SASA, in addition to the molecular surface.

The reference to the algorithm is also printed when you run the program. 
The algorithm used gives basically the same result as the MSMS program 
from Scripps.

>>> How is the DGsolv calculated by g_sas? and the areas ? which algorithm?
>>> where is the code? reference?
>> The code would be in g_sas.c, would be my guess.
> The reference is in the code.
>      "D. Eisenberg and A. D. McLachlan",
>      "Solvation energy in protein folding and binding",
>      "Nature",
>      319, 1986, "199-203"
> This method is completely different from the way nonpolar solvation free 
> energy is calculated in implicit solvation models such as GBSA, which is 
> based on the true SASA. The method of Eisenberg seems more detailed 
> though, because it attributes different weights to surface patches 
> depending on the type of the underlying atom. It would be interesting to 
> know why this method has not been more widely used.

This free energy estimate is close to useless, but easy to compute.
When using Amber atom types it would also be possible to use a slightly 
more modern variant (JPCB 105 (2001) 5055), which is not necessarily a 
lot better though.

> Best,
> Michel

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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