VMD-L Mailing List

From: Dennis N Bromley (dbromley_at_uw.edu)
Date: Mon Sep 22 2014 - 12:52:59 CDT

I just use simple bash scripts to concatenate my pdb files together using
the MODEL and ENDMDL tags. Works well in VMD although the frame numbers
are the model numbers, so you need to convert those to trajectory times
yourself (which is trivial if you are sampling every 10 ps or something).
hope this helps
-denny-

On Mon, Sep 22, 2014 at 5:55 AM, Aref Takiden <
aref.takiden_at_mailbox.tu-berlin.de> wrote:

> Hi,
>
> I would like to merge several pdb-files into one dcd-like-file, in such
> away, that at the end, I could see for example the changes in the bond
> length of the different snapshots(pdb-files) as a graph in the label-window
> of vmd.
>
> I tried the script animatepdbs.tcl (link:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/animatepdbs.tcl),
> but it loaded only the first file in spit of that it read the names of the
> other files. I tested that by adding the command “puts $filename” at the
> end of the for-loop.
> So in other words I had only one frame in my main window of vmd.
>
> I am thankful for any help.
>
> Best regards,
>
> --
> M. Sc. Aref Takiden
> Technical University of Berlin
> Institute of Chemistry
> AG Mroginski
> Straße des 17. Juni 135
> D-10623 Berlin
>
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