VMD-L Mailing List

From: Ranyere Deyler (ranyere_at_gmail.com)
Date: Mon Apr 05 2010 - 11:33:46 CDT

Hello, i tryed that and didn't work. I generated the nanotube, then, in
tkconsole i typed:

package require topotools 1.0
topo retypebonds

and to verify that the bonds had been recognized i typed:

topo numbonds

And it did gave the right value, 156 bonds. So i tryed:

set sel [atomselect all]
$sel writepdb file.pdb
$sel writepsf file.psf

And nothing. Looking at the console it gave this message:

WARNING: PSF file is incomplete, no angles, dihedrals, impropers, or
cross-terms will be writen.

So, it didn't wright down anything, not even the bonds. I tried everything
but it always generate a wrong psf file. If you have another idea i
apreciate. Thanks a lot.

Ranyere Deyler Trindade

On Mon, Apr 5, 2010 at 11:52 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>
> cheers,
> axel.
>
> > 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 akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>