VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 08 2007 - 14:00:49 CDT

Hi,
  I don't know what algorithm the GETAREA web page is using.
The values you get from the different programs often have to do with the
radii assigned to the atoms, so that may be a reason for differences.
The default number of sample points used by VMD is currently 500, which
should give you results within under 1% of each other for different
random seeds.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 08, 2007 at 12:17:12PM -0400, Michael S. Marlow wrote:
> I am using VMD to measure the per atom SASA for a protein. I have noticed the
> -samples parameter significantly impacts the output values; it seems to plateau
> around 500 (which I think is 10X the default value). Is there an
> optimum value (computation speed is not an issue in my case) I should use?
>
> Also, I am getting significantly different values than the GETAREA web
> application (http://pauli.utmb.edu/cgi-bin/get_a_form.tcl). Is there a
> fundamental difference between the two algorithms?
>
> Thanks for all you input,
> Mike
> --
> Michael S. Marlow, Ph.D.
> Department of Biochemistry and Biophysics
> University of Pennsylvania 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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