From: Axel Kohlmeyer (
Date: Fri Dec 31 2010 - 04:54:08 CST

On Fri, Dec 31, 2010 at 5:11 AM, Ramya Narasimhan <> wrote:
> I tried to convert the dcd file to pdb after loading in VMD. When I loaded
> the psf and dcd files, the peptide structure is fine. But after saving the
> coordinates, some of the bonds are missing and some additional bonds are
> seen in the newly written pdb files. How to get rid of this error?

pdb files generated by VMD don't contain bonding information.
when you load the file, the bonds are recomputed from the
element information inferred from the atom names.
the result may not be consistent with what you expect.
if you first load a .psf file with the correct topology information
and then load the .pdb file, then it should look the same as
before, since the bonding information is taken from the .psf.


> Thanks in advance for any comments/suggestions.
> --
> Ramya.L.

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