From: Axel Kohlmeyer (
Date: Mon Jan 03 2011 - 04:58:45 CST

On Mon, Jan 3, 2011 at 12:50 AM, Ramya Narasimhan <> wrote:
> 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?

the problem is not with VMD, it is what you expect from what you give it.

it doesn't matter where the coordinates are coming from.
VMD can only show you the information that you give it.
if you load a .psf/.dcd combo you have _more_ information
than in the .pdb file alone. if you throw away information,
you cannot expect that it will be there when you look for it again.

 the bonding information reconstructed when loading the .pdb file
alone depends on a lot of guessing and several assumptions. if
your coordinates do not conform to those, you will get something
that is different from the .dcd/.psf. as it told you, if you load the
.psf file first and then a .pdb file, you should see the same.

before you continue to claim that this is VMD's problem, please
provide proof, that there _is_ a problem that is not a case of PEBCAC.


> Thanks in advance for any comments/suggestion.
> Ramya.L.

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