VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 01 2012 - 13:53:58 CST

Hi,
  Was your selection set to "all" when you saved the structure?
You didn't say which version of VMD you're using, but having that
information would also be very helpful.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 01, 2012 at 07:26:31PM +0100, R. Charbel Maroun wrote:
> Hi everybody,
>
> The coor file produced by NAMD is actually a pdb file. Have to rename
> it to pdb before using it again in NAMD as input. Otherwise you'll get
> error messages.
>
> Also, for an unknown reason, trying to save a coor file of a
> protein-membrane-solvent system (85000 atoms) as a pdb file in VMD
> using the Save Coordinates/Trajectory menu saves only a chunk of the
> system, i.e., the protein, the solvent and part of the bilayer are
> missing ! I tried several things, such as saving a mol2 file, loading
> it into VMD and then trying to save it as pdb, but again, only part of
> the system is saved. Is this a bug ? I tried to find also a TCL/TK
> line command that could save my molecule, but couldn't find one. I
> went over the VMD list and found nothing about it.
>
> Thanks for the help.
> -----------------------------------------
> R. Charbel MAROUN, Ph.D., H.D.R.
> Centre Interdisciplinaire de
> Recherche en Biologie (CIRB)
> CNRS UMR 7241/INSERM U1050
> Collège de France
> 11 Place Marcelin Berthelot
> 75005 PARIS
> Tél: +33 1 44 27 14 91
> Fax: +33 1 44 27 14 76
> e-mail charbel.maroun_at_inserm.fr
> charbel.maroun_at_college-de-france.fr
>
>
>
>
>
>
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>
>
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-- 
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