VMD-L Mailing List

From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Fri Mar 29 2013 - 17:19:18 CDT

Thanks,
Working like a charm now!

-Yarrow

> Hi,
> There's a MUCH easier way: if you use one of the recent versions of
> VMD, you can simply make an atom selection for the part of the
> structure that matches your DCD, and then use "$sel writepsf subset.psf"
> and VMD should generate you a correct PSF file that matches the
> DCD file. You can check this very easily by loading the DCD and
> the new PSF and look at the results.
>
> Cheers,
> John
>
> On Thu, Mar 28, 2013 at 05:34:23PM -0700, Yarrow Madrona wrote:
>> 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
>>
>>
>
> --
> 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