VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 07 2005 - 11:53:12 CST

Ed,
  Since you're using b4, I think that the likely issue is that you
need to add the restrict option to NOT count the surface area of
atoms that border the parts you're excluding from the atom selection.
The same would be true if you had internal cavities that you didn't want
contributing to surface area.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 07, 2005 at 12:49:18PM -0500, Edward Patrick Obrien wrote:
> Hi John,
> Thanks for the quick response.
> The version is:
> VMD for LINUX, version 1.8.3b4 (January 20, 2005)
>
> I've attached a graph of the time dependence of the sasa for
> the protein, sidechains and backbone. I've checked several times
> and I did not mislabel the files:)
>
> Ed
>
> PS- should I use the "restrict" option to correct this?
>
> On Mon, 7 Feb 2005, John Stone wrote:
>
> >
> >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
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > 

-- 
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              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078