VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 05 2002 - 19:29:42 CST

Dear Markus,
  Though VMD does not directly calculate these items, the "Surf" and
"MSMS" solvent accessible / solvent excluded surface programs do calculate
some of these values. If you call them directly, you should be able to
get the information you need. I also believe that the old AlphaShapes
software will do this sort of thing, and there are undoubtably several
other packages that handle this. If you need help getting this done
beyond knowing about the available packages, let me know and I'll
dig up some more details for you.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 04, 2002 at 07:49:02PM +0100, Markus Laub wrote:
> Hello there,
>
> is it possible to calculate the van der Waals volume/surface of a
> molecule using VMD? If so is it also possible to calculate the solvent
> accessible surface/ volume (Richards) and the molecular surface/volume
> (Connolly)?
>
>
> Thank you,
>
> Markus Laub
>
>
> 

-- 
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