Re: topology file for nanotube

From: Axel Kohlmeyer (
Date: Thu Mar 10 2011 - 04:43:37 CST

you left out the improper definitions.

FYI, in VMD 1.9 this feature is included in the
nanotube plugin though the GUI.


On Thu, Mar 10, 2011 at 3:10 AM, Ranyere Deyler <> wrote:
> For simulating Nanotubes, you don't need a topology file. You just have to
> use "topotools 1.1" that it can handle the creation of the psf file just
> fine. Search for the help of the topotools 1.1 on google, and there you'll
> find out how to obtain the psf file, you'll just tell it to guess the bonds,
> angles and dihedrals, and then you just "writepdb" and "writepsf", and it's
> good to run on NAMD. Take a look on the help!
> Cheers.
> Ranyere Deyler Trindade

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:44 CST