VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 21 2010 - 14:09:13 CST

Bernhard,
  The built-in SASA functions in VMD are based on a very simple
monte carlo estimation technique. You can read the actual code here:
  http://www.ks.uiuc.edu/Research/vmd/doxygen/Measure_8C-source.html#l01058

The algorithm used samples the surface area of spheres in the atom
selection, accepting/rejecting them based on whether or not they fall
within the radius of neighboring atoms. This gives you a "union of spheres"
type surface area, which is close but not identical to the area that you
get if you use a "rolling ball" type method, say like what MSMS computes.

Let me know if you have more detailed questions.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 21, 2010 at 09:32:31AM +0100, Bernhard Knapp wrote:
> Hi everyone,
>
> does anyone know which build-in SASA calculation functions are used in
> VMD (in the source it is called via "measure sasa")?
> I would need the proper citation for it but unfortunatly I couldn't find
> a hint for it in the VMD paper.
>
> cheers
> Bernhard
>
> 

-- 
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