[gmx-users] Calculating Molecular Volumes

[Alan Wilter Sousa da Silva]

Try MSMS
(http://www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html)

Such program can calculate molecular volume and area (analytical and
numerical).

Cheers,


On Mon, 2 Dec 2002, Donald E. Elmore wrote:

> Hi--
>
> I was reading in the paper describing the make_hole protocol
> (Faraldo-Gomez, Smith, and Samson, Eur. Biophys. J 2002) that one can
> calculate the molecular volume of a protein structure using HOLE.  (By
> getting the cross-sectional area along one dimension and then integrating
> over that dimension.)  I've used HOLE (v. 2) to calculate pore radii, but
> I couldn't find how to get the area of the whole molecule from the
> documentation.  I'm probably just missing it, but I thought one of you
> might be able to point me in the right direction.
>
> Thanks!
>
> -Don Elmore
>
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-- 
-----------------------
Alan Wilter S. da Silva
-----------------------
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil