From: Josh Vermaas (
Date: Wed Apr 17 2013 - 17:34:14 CDT

If you are satisfied with the number of other terms present in the psf,
all you'd need to do is add a line like:
topo guessbonds
and then write the psf file with animate. I'd be very careful though, as
psfs are easy to screw up unintentionally when building them by hand. As
others have pointed out on this list, there is a perfectly serviceable
nanotube builder (
and the usual solvation schemes
( will get you a
nanotube in water without needing to rebuild bond tables.

On 04/17/2013 02:54 PM, Anurag Sharma wrote:
> Hi,
> 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