From: Joshua Adelman (jla65_at_pitt.edu)
Date: Tue Oct 19 2010 - 07:30:16 CDT

Hi Surendra,

Are you asking how to extract the C-alpha atoms from your DCD file, or how to run PCA on the resulting coordinates, or both?

To extract the CA atoms, I like using catdcd (http://www.ks.uiuc.edu/Development/MDTools/catdcd/) with the appropriate index file to grab the CA atoms. Many of the methods that have been suggested previously on the list to run PCA also allow you to make atom selections in-program, so you might not have to do this in two steps. This question has been asked and answered countless times on both the VMD and NAMD lists. Archives of both lists are searchable through their respective websites, so I would start there, since I and others have already offered up solutions to this very problem several times in the past.

Best of luck,
Josh

On Oct 19, 2010, at 5:58 AM, surendra jain wrote:

> Hi everyone,
>
> I have a system with protein, water and lipid. I want to extract the protein backbone (C alpha) coordinates from the dcd file and run a PCA on them. Can someone tell me how to do this in VMD/NAMD.
>
> Thanks in advance.
>
> Surendra
>