From: Axel Kohlmeyer (
Date: Mon Apr 05 2010 - 09:52:55 CDT

On Mon, 2010-04-05 at 10:58 -0300, Ranyere Deyler wrote:
> Dear VMD Users,
> I generated a carbon nanotube by the plugin in VMD. Well, it
> recognizes the bonds on the nanotubes but when i give the
> set sel [atomselect all]
> $sel writepdb file.pdb
> $sel writepsf file.psf
> it doesn't add any bonds on the psf file. It shows the bonds on the
> console when you create the nanotube but when you write down the psf
> file it doesn't.

can you please try if issuing the "topo retypebonds" command
after building the carbon nanotube solves the bond writing issue.

> So i'm wondering if there's a better way of generating the psf of the
> CNT.
> I tryed using the AutomaticPsf Builder but it was not successful, it
> gives some erros, it says that 'CNT' is not parametrised. And if

psfgen (which autopsf is a front end for) cannot work for these
kinds of systems.


> someonet has the proper topology file for a carbon nanotubes (as the
> ones in the tutorial water trough nanotubes, that already gives the
> psf but it doesn't have the topology file that generated it), i would
> apreciate.
> Thanks a lot
> Ranyere Deyler Trindade

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