VMD-L Mailing List

From: Mert Gür (gurmert_at_gmail.com)
Date: Thu Mar 28 2013 - 20:50:23 CDT

I was going to suggest you to save the protein coordinate of any selected
frame as a pdb. Load this pdb. Delete the frames and the load your dcd for
the protein only. This should work( It works for me). However, in your next
e-mail I think you point out that it did not work well. John explained in
his e-mail what I was going to suggest you so I will skip my dcd loading
suggestion.

Best,
Mert
On Mar 28, 2013 8:36 PM, "Yarrow Madrona" <amadrona_at_uci.edu> wrote:

> Hi Mert,
>
> I am having trouble making a new psf that matches the truncated dcd I
> made. I would be happy to know how to trouble-shoot this. Thanks.
>
> -Yarrow
>
> > Are you able to load a single trajectory? If yes there is a solution.
> > Best,
> > Mert
> > On Mar 28, 2013 5:24 PM, "Yarrow Madrona" <amadrona_at_uci.edu> wrote:
> >
> >> 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
> >>
> >>
> >>
> >>
> >
>
>
> --
> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
>
>
>