From: Axel Kohlmeyer (
Date: Wed Aug 12 2009 - 09:40:08 CDT


On Wed, Aug 12, 2009 at 9:27 AM, Liang, Linus H.<> wrote:
> Dear all,
> I'm working with a carbon nanopore structure and I'm trying to remove all the bonds between the carbons. However, when I uploaded a new psf file with 0 bonds angles and dihedrals, VMD automatically bonds the carbon atoms back together when I load up the pdb file.

the .pdb file does not contain any bond information, thus VMD guesses it
based on guessed element radii. you can turn the guessing off when loading
from the command like or prepare a .psf file to go with the .pdb file which
has explicit bonding information.


> Thanks for your help in advance,
> Linus

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.