VMD-L Mailing List
From: R. Charbel Maroun (charbel.maroun_at_inserm.fr)
Date: Wed Feb 01 2012 - 12:26:31 CST
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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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