From: Axel Kohlmeyer (
Date: Sun Dec 20 2009 - 09:55:04 CST

On Sun, Dec 20, 2009 at 9:46 AM, leila karami <> wrote:
> Dear Axel
> I attached my pdb file containing superimposed structure.
> As you said I loaded topology file first and then the coordinates on top of
> that. but problem was not solved

remember the "garbage in, garbage out" principle.
your pdb file is actually two pdb files, but they are not
separated by an END record, so VMD will try to load
both into one "molecule" and then guess the bonds
based on that. just add an END record after the TER
records and the pdb plugin in VMD will read it as two

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.