From: Joshua Adelman (jla65_at_pitt.edu)
Date: Sun Sep 23 2012 - 19:01:42 CDT

On Sep 23, 2012, at 2:48 PM, Venkata Mandala wrote:

> Hello--
>
> I was looking for a way to extract the exact coordinates of all the atoms of a protein simulation for the whole length of the simulation, and then using the coordinate data to analyze different parameters. Is there any way I can extract the individual coordinates from the DCD file that has the simulation data?
>
> Thanks!
> Shiva
> Oberlin College, OH

Hi Shiva,

You can certainly extract and analyze the coordinates in a DCD file using VMD and a bit of Tcl scripting (take a look at the manual), and many common operations are available through that interface. It would be especially helpful to familiarize yourself with the atom selection syntax:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node121.html

There are other options outside of VMD to access the coordinates from a DCD to do analysis. Personally, I feel more comfortable doing complex numerical manipulations in Python, so I often use MDAnalysis (http://code.google.com/p/mdanalysis/) or Prody (http://www.csb.pitt.edu/prody/).

If you give a sense of what you are trying to do specifically, you might get more explicit advice.

Best wishes,
Josh