VMD-L Mailing List

From: Ranyere Deyler (ranyere_at_gmail.com)
Date: Mon Apr 05 2010 - 08:58:55 CDT

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.
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 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