From: Axel Kohlmeyer (
Date: Wed Sep 07 2011 - 14:55:10 CDT

On Wed, Sep 7, 2011 at 2:49 PM, winardi, erik <> wrote:
> Dear VMD community,
> I have trajectory files which need to be visualize. They are in .pdb and
> .xyz format.
> I do not have the initial configuration data for these trajectory files.
> I tried loading these trajectory files into VMD and playing around the
> Graphic Representation Tools.
> However, I couldn't get the atoms to appear. I chose the VDW molecule type.
> Is it possible to visualize the atoms and bonds only from .pdb or .xyz files
> ?
> or do I need to get the initial configuration too ?

no. both file formats, .xyz and. pdb, contain coordinate information.

please have a close look at the VMD console
and check if there are any error messages.

VMD will do a best effort to parse files according
to the available "standards" and some commonly
used variants, but if the format strays too far, the
corresponding plugin may reject reading the files.

if there is no message visible, please provide small
example files demonstrating the issue.


> Thanks,
> Erik Winardi

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.