VMD-L Mailing List

From: Michael S. Marlow (marlowms_at_mail.med.upenn.edu)
Date: Tue May 08 2007 - 11:17:12 CDT

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