From: Katherine Parra (
Date: Fri Sep 18 2009 - 12:04:04 CDT

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.