From: Nguyen Hoang Phuong (
Date: Wed Apr 03 2002 - 10:20:54 CST

Dear Stone,

I have tried with two ways: Using your script file animatepdbs or
concatenate all of the PDB files into one file (with END between
them). Unfortunately, both methods don't work. I attach here the two pdb



> 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.
> Thanks,
> 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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