From: Ramya Narasimhan (
Date: Sun Jan 02 2011 - 23:50:43 CST

I have the correct information in the psf file and I have checked it by
loading individual pdb file also. The actual problem arises only when I save
coordinates as pdb after loading the dcd over psf file. While viewing the
trajectory it is perfect. Actually the trajectory is from MC simulation. Can
anyone help me to overcome this problem?

Thanks in advance for any comments/suggestion.


On Fri, Dec 31, 2010 at 4:24 PM, Axel Kohlmeyer <> wrote:

> 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.
> axel.
> > Thanks in advance for any comments/suggestions.
> > --
> > Ramya.L.
> >
> --
> Dr. Axel Kohlmeyer
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.