VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 28 2013 - 20:50:42 CDT

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/