VMD-L Mailing List

From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Sun Sep 23 2012 - 18:18:10 CDT

What exactly would you like to do with the coordinates? There are a lot of ways to extract information directly from the dcd files via tcl scripting without having an explicit readout of the atom coordinates. If you do need coordinates, you can use "get" has Maria suggested or you can write pdb files of individual frames. I'd think though that there would be some way to directly preform the analysis you're interested in if you give some more specifics.

-Erik
________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Maria Antonieta Sanchez Farran [mfarran_at_engr.psu.edu]
Sent: Sunday, September 23, 2012 3:04 PM
To: vmandala_at_oberlin.edu; vmd-l_at_ks.uiuc.edu
Subject: RE:vmd-l: Getting trajectories from DCD files?. .

Hi Shiva,

You can extract coordinates by using the get { x y z} command in tcl. If
you apply this to an atom selection ($sel get {x y z}), you will obtain
a list of lists. Make sure that you manipulate lists appropiately using
the "lindex" command. If you are starting, manipulating lists can be a
bit confusing, so I would recommend you to get famililar with that
first. Take a look to this link - it explains this very clearly:
http://www.csb.yale.edu/userguides/graphics/vmd/ug/node181.html.

Another alternative, is to use MATDCD, which is a MATLAB package for
reading DCDs: http://www.ks.uiuc.edu/Development/MDTools/matdcd/

Hope this helps,
Maria Antonieta

Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer