VMD-L Mailing List

From: Sean T Kigerl (skigerl_at_ucsd.edu)
Date: Tue Aug 14 2012 - 00:43:26 CDT

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!

Sean Kigerl