VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Apr 24 2008 - 08:43:19 CDT

On Thu, 24 Apr 2008, politr_at_huji.ac.il wrote:

RP> Dear users and developers,
RP> I was working with perl script that finds the closest distance between each
RP> water molecule (OH2) and my protein. The script is checking all atoms of my
RP> protein. When I tried to use the command WITHIN OF ( set close_wat
RP> [atomselect top "name OH2 and within $r of (protein or resname ACE)"] ) I
RP> got the different number of water molecules at some predefined distance
RP> ($r). I got less water molecules by using VMD command than by my perl
RP> script. In addition, the distances are not the same by two methods for the
RP> same atoms.
RP> Do someone has an explanation to this problem.

a bug in your perl script?

axel.

RP> Thanks
RP> Regina
RP>
RP> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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.