VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 31 2003 - 10:24:41 CST

Dear Rukman,
  It should be possible to calculate this via MSMS or Surf somehow,
but there's not presently an interface in VMD to query this information
from the programs. You could certainly write a script to drive Surf or
MSMS in computing individual surface for each frame, the difficulty
lies in convincing them to calculate SASA for each frame, and somehow
parsing this out of their text output. Perhaps your best option would
be to send an email to Michel Sanner, the author of MSMS and ask him
for a suggestion. Worse case, I think that you could do this by writing
a script in VMD to cause VMD to write out a PDB file of an atom selection
for each frame, and subsequently translating this into valid input for MSMS.
At that point, the script could just exec MSMS and do whatever is necessary
to calculate the SASA you're interested in. Let us know if you need help
with the VMD side of writing such a script.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 31, 2003 at 06:59:16PM +0900, Rukman Hertadi wrote:
> Hi,
>
> Is there any script available for VMD to calculate the solvent accessable
> surface area (SASA) from the trajectory file. The available free software
> only able to do the calculation for a single pdb file.
>
> Thanks in advance.
>
> Rukman Hertadi
>
> Laboratory of Biodynamics
> Graduate School of Bioscience and Biotechnology
> Tokyo Institute of Technology
> 4259 Nagatsuta-cho, Midori-ku, Yokohama,
> Kanagawa 226-8501, Japan.
> Phone: +81-45-924-5739
> FAX: +81-45-924-5806
> email: rhertadi_at_bio.titech.ac.jp
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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