From: Axel Kohlmeyer (
Date: Mon Apr 05 2010 - 14:30:21 CDT

On Mon, 2010-04-05 at 16:06 -0300, Ranyere Deyler wrote:

> 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

that would mean that you don't need bonds either, right?

> 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?

there is an internal flag in VMD that is being set if you
read in or modify bond or angle definitions. that flag is
being queried upon writing. topo retypebonds triggers this
flag, even though a psf file doesn't know about bond types.

> 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.

i just tried it for myself and it works as advertised.


> Thanks a lot.
> Ranyere Deyler Trindade

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