From: Axel Kohlmeyer (
Date: Wed May 19 2010 - 14:33:01 CDT

hi francesco,

On Wed, May 19, 2010 at 2:52 PM, Francesco Pietra <> wrote:
> Hi:
> From the manual and the archives I was unable to figure out how to
> prepare psf/pdb for simulation by cutting the bond of a given atom
> with a ligand. That is, I would like to start with no such bond, a

please explain a little more detailed what you are looking for.
is it that you want to remove a specific bond between two
atoms from the .psf file? in that case i have a suggestion.
otherwise explain what exactly you want to know.


> situation that occurs under certain experimental conditions. I can
> figure out that the bond length at issue - and rotations - should be
> constrained, but  I can't imagine how in the framework of VMD.
> Thanks for suggestions
> francesco pietra

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