VMD-L Mailing List

From: Ronald Salesky (rsalesky_at_unm.edu)
Date: Mon Apr 05 2010 - 14:33:44 CDT

The NAMD tutorial "Simulation of Water Permeation through
Nanotubes" may prove helpful. There are CHARMM22 parameter
file for CNTs and a CNT.psf file you can examine.

On Mon, 5 Apr 2010 13:33:46 -0300
  Ranyere Deyler <ranyere_at_gmail.com> wrote:
> 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.
>>
>>