From: Axel Kohlmeyer (
Date: Tue Aug 14 2012 - 07:25:42 CDT

On Tue, Aug 14, 2012 at 7:43 AM, Sean T Kigerl <> wrote:
> Hello all,
> I used the inorganic builder plugin to create a silicon nitride nanopore
> (for which I now have pdb and psf files). I also used the molefacture
> plugin to build a benzene ring attached to a nitrogen atom (for which I
> now have pdb, psf, topology and parameter files). My question is how would
> I create a pdb/psf with the nitrogen (from the benzene ring) attached to
> one of the silicon atoms in the inside of the nanopore? (Essentially
> functionalizing the nanopore with a benzene ring) Any suggestions would be
> greatly appreciated!

merge the two psf files and the two pdb files.
load the combined topology and coordinates,
move molecule, if needed, and then add the bond.
this is probably easiest done with the mouse,
but you can script it. each atom has a list of atoms
that it is bonded to, so you have to add two entries.
if you are lazy you can use the wrapper in topotools.


> Sean Kigerl

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.