VMD-L Mailing List

From: Ranyere Deyler (ranyere_at_gmail.com)
Date: Mon Apr 05 2010 - 15:47:24 CDT

Hello again, and thanks again for your help. Well, it did work now, the
"topo retypebonds". I don't know why it didn't work before, must have done
something wrong. But, it's good to know that it can be done like that. I
would spend lots of time doing it manually.
So, Axel, you were saying, is it possible to guess the angles and dihedrals
using "topotool" for the CNT? And them write down the psf file the same way?
Do I need to enter with some parameter? Or it does it automatically?
Because, when i'll be needing the CNT to be not fixed i would need those in
the psf file as well.

Thanks a lot.

On Mon, Apr 5, 2010 at 4:33 PM, Ronald Salesky <rsalesky_at_unm.edu> wrote:

> 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.
>>>
>>>
>>>
>