VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 07 2005 - 11:39:06 CST

Edward,
  Which exact beta version did you encounter this behavior with?
We fixed a SASA calculation bug back in beta 3, so if you have a
version older than that, that's the likely cause of the problem.
Let me know which version you were testing with.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 07, 2005 at 12:26:16PM -0500, Edward Patrick Obrien wrote:
> Hi All,
> I downloaded the VMD v1.8.3 beta version to use the SASA command to
> measure solvent accesible surface area.
>
> I can analyze my dcd's with it, BUT I am getting a physically
> unreasonable result. The result is that the Surface area of the sidechains
> is larger then the Surface area of the protein as a whole!!!
>
> The SA,protein = SA,sidechains + SA,backbone, should be true. But
> instead I find:
> SA,protein < SA,sidechains + SA,backbone
>
> with the SA,sidechains > SA,protein.
>
> My initial guess is the sasa command is not taking into account the
> excluded volume of the backbone when it measures the surface area of the
> sidechains, and vice-versa.
>
> Any suggestions about how to get self-consistent results?
>
> Thanks!
> Ed
>
> PS- for srad I use 1.4, is this resonable? 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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