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

[Michel Cuendet]

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.
>>
>> 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.

Best,
Michel

-- 

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Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
http://ludwig-sun1.unil.ch/~mcuendet
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