VMD-L Mailing List

From: Ranyere Deyler (ranyere_at_gmail.com)
Date: Mon Apr 05 2010 - 14:06:38 CDT

Hello again. Well, in my case i just need the the bonds, because i'm gonna
fix the atoms of the nanotubes. So the angles and dihedrals won't be needed.
But the problem still relies on the fact that it's not writing down the psf
file correctly. It shows the the bonds, via "topo" but it doesn't export
them.
Nothing seem to work. Wouldn't it be because the bonds shown are just for
representation?

And correcting what i said before, i really used
"set sel [atomselect top all]"

and not
"set sel [atomselect all]" as i said before. So that's not the problem.

Thanks a lot.

Ranyere Deyler Trindade

On Mon, Apr 5, 2010 at 1:56 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Mon, Apr 5, 2010 at 12:33 PM, Ranyere Deyler <ranyere_at_gmail.com> wrote:
>
> > 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.
> >
>
> the message is not important. this message is only printed
> when you don't write out angles and dihedrals. it doesn't say
> anything about the bonds. have a look at the psf file itself!
>
> you can in principle silence the message by using:
> topo guessangles
> to generate the corresponding angle definitions, similarly
> for dihedrals and impropers, but you have to check the literature
> on which definitions would be a good idea to include
> or whether it would be sufficient to just do a position
> restraint on the CNT atoms.
>
> in general, if you want a realistic description of a CNT
> you should use an AIREBO or Tersoff many body
> potential and those don't need any of the two.
>
> cheers,
> axel.
>
>
>
> > 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.
> >>
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>