From: Norman Geist (
Date: Thu Feb 12 2015 - 02:35:21 CST

You can use either the “VMD Main->File->Save Coordinates” GUI


or something like:


set sel [atomselect top “resid 5”]

$sel writedcd myres5.dcd

$sel delete


Norman Geist.


From: [] On Behalf Of Monika Madhavi
Sent: Thursday, February 12, 2015 7:56 AM
Subject: vmd-l: how to select a particular molecule


Dear all,

I need to select all the atoms of a particular water molecule from a dcd file and write it's coordinates to a separate pdb/dcd file. Can I do this using atomselect in vmd tcl? I tried the following command but it doesn't work.

set sel [atomselect top {resid 5}]

Thank you.


W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.