From: Anurag Sharma (
Date: Wed Apr 17 2013 - 14:54:35 CDT


  I am working with a solvated Carbon nanotube model. I have deleted some of the water molecules in the model and try to generate psf file for this new model using topo tools. I used animate write psf script to create this psf file. But in the generated psf file the bonds are missing (0 bonds). Though when I used guess bonds and then numbonds in tcl it shows the correct no. What could be the possible solution for this problem. Please suggest.

Angles, dihedrals and impropers are present in the generated psf file. All other parameters are also present. Only bonds are missing.

Thank you

Anurag Sharma