From: Anurag Sharma (
Date: Wed Apr 17 2013 - 19:37:42 CDT

Hi Josh,

    I have tried the solution in the link but unfortunately it is also not working. VMD hangs everytime I use this script. Do you think any other way to solve this problem.

Thank you

Anurag Sharma

From: Josh Vermaas []
Sent: Wednesday, April 17, 2013 6:32 PM
To: Anurag Sharma
Subject: Re: vmd-l: No bonds in the generated psf file

Hmm, you appear to have stumbled into a bug with how psfs are written, as my tests show that it fails to write them out too if I use guessbonds. If you are just trying to delete waters, the psfgen userguide (<>) has a handy little section devoted to this very topic, and you'd save yourself quite a bit of heartache until someone fixes the psf writer.

On 04/17/2013 05:52 PM, Anurag Sharma wrote:


    I have tried the topo guessbonds command. It gave me the right no. Of bonds which I verified with topo numbonds but when I used animate write psf command and generate psf file. There are no bonds mentioned in that psf file ( all other parameters are present). That means the problem I am facing is in animate command.
I am deleting water molecules from inside the tube here.


Anurag Sharma

Sent from my iPhone

On Apr 17, 2013, at 5:42 PM, "Josh Vermaas" <><> wrote:

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:


  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