Date: Thu Apr 24 2008 - 08:22:23 CDT

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