From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Thu Mar 28 2013 - 19:34:23 CDT

Hi John,

Thank you for your help.

Using CatDCD to create a sub-selection DCD was pretty straight forward and
I now have a much smaller dcd that covers the 17 I previously had.

However, I am wondering: if I generate a new PSF (using PSFgen) with just
those atom selections, then will they be consistant with the DCD? I'm
assuming the indicies would change. How do I keep the same indicies from
the original PSF to be consistant with the DCD? I tried to just feed in a
truncated PDB which I'm not surprised didn't work as the bonds and angles
all collapsed.

-Yarrow

>
> Hi,
> You will need to use a combination of VMD and CatDCD together to
> achieve what you're after. You can use VMD to create PDB/PSF files
> that contain the subset of the system you're interested in, and you
> can use CatDCD to process all of your DCD files to create subset
> versions of those. The indices CatDCD wants are atom indices only,
> as CatDCD has no knowledge of higher level structure organization,
> only atom indices. If you were able to load one DCD at a time into
> VMD, you could also have VMD do all of this with a short script,
> but it is good to learn how to use CatDCD when working with
> huge files since it has a much lower RAM requirement as it only
> reads and processes a single trajectory frame at a time.
>
> Cheers,
> John
>
> On Thu, Mar 28, 2013 at 03:46:17PM -0700, Yarrow Madrona wrote:
>> 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
>>
>>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
>

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