From: Thomas Evangelidis (
Date: Sat Sep 19 2009 - 09:04:36 CDT

Hi Katherine,

lets say you want to count all the waters(TIP3) within 5 A of resids
1-50 taking into account waters in the nearest periodic cells, then
the command should be:

llength [[atomselect top "(oxygen pbwithin 5 of (protein and resid 1
to 50)) and resname TIP3"] list]

I have an alpha version of a plugin to truncate trajectories and keep
only a specified number of waters within R Angstroms of an
atomselection, it might be helpful to your analysis.


> Dear VMD users:
> My sytem contains 18 proteins in a unit cell. I also have several 20ns
> trajectories (*.dcd) of this system.
> I would like to calculate the distribution of the water molecules around
> each one of the proteins and around the different amoinoacids that compose
> them during the trajectories.
> I've been trying to find another VMD mail list posted message containing
> this question and somewhere in the VMD user's guide but I haven't found
> anything related.
> I've worked with some scripts in VMD, using the atomselect command and doing
> loops along trajectories.
> What I need is some help with the right command to count water molecules
> (TIP3) around a specific part of the protein.
> Thank you in advance.
> KP

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