Re: water molecules in channel protein

From: Roman Petrenko (
Date: Wed Aug 05 2009 - 11:59:21 CDT

if your pore is oriented along z direction there is an easy way to do it.

assuming pore is in the interval [-15, 15] of z-axis, for each frame
you can count number of waters in this slab:

set wsel [atomselect top "name OH and z>-15 and z<15"]
set nw $wsel num
puts $nw

On Wed, Aug 5, 2009 at 11:57 AM, Narender Singh Maan<> wrote:
> Hello, I was wondering if someone could please let me know on what would be
> the best way to study channel water molecules, i.e. i want to know how to
> extract the total number of water molecules, present inside the channel
> protein, from each frame.
> Thank you
> naren

Roman Petrenko
Physics Department
University of Cincinnati

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