From: Joshua Adelman (jadelman_at_berkeley.edu)
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:
http://www.ks.uiuc.edu/Development/MDTools/catdcd/
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.
Josh
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
>
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Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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