From: Axel Kohlmeyer (
Date: Mon Sep 27 2010 - 10:29:25 CDT

On Mon, Sep 27, 2010 at 9:42 AM, yan zhang <> wrote:
> Hi, sir ,
> The PDB file of the protein which was prepared to run NAMD contains missing
> atoms .

hmmm... interesting way to phrase this. a file
that contains atoms that a missing. ;-)

> How can i add these missing atoms by VMD?

VMD itself is only a viewer. if the missing atoms are
part of known residues for which at least some part
exists in the pdb file, then they can be reconstructed
(to some degree) from internal coordinates in the force
field topology files through the psfgen plugin.

if whole residues are missing, you have to use
some other tool.


> Thanks,
> Sweety

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