From: Axel Kohlmeyer (
Date: Wed Apr 23 2008 - 09:04:00 CDT

On Wed, 23 Apr 2008, wrote:

RP> Dear All,

dear regina,

RP> I'm trying to find some command that allows me to find the smallest
RP> distance between water molecule (let say oxygen) and my protein.

there is no predefined command for that,
you'll have to write some more complex scripting.

essentially you have to build a distance matrix and
find the smallest elements, but depending of the size
of your problem that can be time consuming so you
should try hard to limit the number of rows and columns
(i.e. water oxygen positions and protein atom positions)
as much as possible before doing that.


RP> Regina

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.