VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 31 2003 - 18:01:25 CDT

Hi guys,
  If you guys can help me out by providing test files in the various
formats, I think I can put together an appropriate plugin for reading
all of these variations of files in short order. I talked to David Case
about some of this today while I was visiting Scripps, and he had some
good suggestions that I'm going to try when I return from Siggraph.
I'll email you guys about getting test data when I get back.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 31, 2003 at 10:44:32PM +0200, Teletcha Stphane wrote:
> Le jeu 31/07/2003 à 21:22, caldwell_at_heimdal.compchem.ucsf.edu a écrit :
> > Please be aware that Amber has two coordinate file formats:
> >
> > inpcrd/restrt is the single structure file that contains the
> > high resolution coordinates. It is used to start/restart
> > minimization/dynamics runs in conjuction with prmtop.
> >
> > mdcrd is the multiple structure (lower resolution) trajectory file.
> >
> > They are NOT interchangeable.
> >
> > VMD reads only mdcrd files. If you want to look at a single
> > structure from your inpcrd/restrt file then convert it to
> > a pdb file with one of the utilities included in Amber.
> >
> > jim
>
> I do not totally agree on your point.
> It is possible to read both formats in vmd : mdcrd natively (i.e. using
> crd selector) and inputcrd when the first line is removed, like this it
> can be parsed by vmd as an mdcrd, although it is not.
> For the rst file, it is more complicated since there are also velocities
> and in that case vmd's reader doesn't simply read it coherently.
>
> Stéphane
> --
> Teletchéa Stéphane <steletch_at_biomedicale.univ-paris5.fr> 

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