VMD-L Mailing List

From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Thu Mar 28 2013 - 17:46:17 CDT

I have been trying to use catdcd but I am not sure the command for only
including a specific residue. Do you need to list all index numbers for
every atom in the residue?

Sorry if this is a dumb question but I cannot find this explained in the
online description of catdcd.

-Yarrow

> You cannot. Use catdcd for it. Axel.
> ------Original Message------
> From: Yarrow Madrona
> Sender: owner-vmd-l_at_ks.uiuc.edu
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: vmd-I: remove water, protein from a dcd
> Sent: Mar 28, 2013 9:45 PM
>
> Hello,
>
> I have 17 long trajectories (50Gigs total). I really am only interested in
> what is happening to a heme cofactor and ligand. I would like to strip
> everything else from the PSF and from the DCD.
>
> The reason for this is, I can't load this dcd onto my laptop and creating
> a summary-shorter dcd is not an option.
>
> My question is: How can I strip the dcd in the command line in VMD.
>
>
> --
> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
> 

-- 
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697