[gmx-users] Calculating Molecular Volumes

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Mon Dec 2 13:29:43 CET 2002


Such program can calculate molecular volume and area (analytical and


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

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