[gmx-users] Calculating Molecular Volumes

Donald E. Elmore elmore at its.caltech.edu
Mon Dec 2 10:43:45 CET 2002


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.


-Don Elmore

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