From: John Stone (
Date: Wed Apr 03 2002 - 09:48:14 CST

Dear Phuong,
  How are you loading your collection of PDB files into VMD?
If you concatenate all of the PDB files into one file, with
"END" marks between them, you should be able to get VMD to
read the concatenated PDB file as a trajectory. If you have
any strange bonds in your structure when loading just the PDB,
the best course of action is to supply VMD with a topology file
such as a PSF file, so that it doesn't have to guess the bonds
with a distance based search. You can create a PSF file with the
standalone 'psfgen' program that comes with NAMD, or with the
psfgen package that was included as part of the VMD 1.7.1 release
for several of the supported VMD platforms. Alternately, you can
use other programs like X-PLOR or Charmm to do this.

Let us know if you have more questions.

  John Stone

On Wed, Apr 03, 2002 at 01:24:16PM +0200, Nguyen Hoang Phuong wrote:
> Dear VMD Users,
> I would like to animate the colection of the pdb files but VMD draws the
> strange bonds between water molecules. For each pdb file, everything is
> fine. Does anyone have the experience about this? Thanks in advance.
> Phuong

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