Re: Selectively write atoms to dcd files

From: Joshua Adelman (
Date: Mon Apr 13 2009 - 12:32:52 CDT

catdcd is a command line tool, so there is no need to load your dcd
into VMD. Everything you need can be found here:

There are examples listed, but in general to do what you're look for:

catdcd -o system_without_wat.dcd -i protindex.ind system_with_wat.dcd

You can create the index file in VMD by loading in your original pdb
(entire system) and doing
set A [atomselect top "protein"]
$A get index

Then copy the results into a textfile.


On Apr 13, 2009, at 10:20 AM, DimitryASuplatov wrote:

> Hello,
> I want to remove WATER from my dcd file and write only the protein
> coordinates. As I understand it could be done with catdcd utiluty
> which
> is now part of VMD package.
> Could you give me a tip on how could this be done without loading the
> complete dcd into the vmd graphics environment since my system is very
> large.
> Thanks

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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