VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Tue Aug 14 2012 - 07:11:33 CDT

Hi

I really don't know much about this but I think you'll be able to get some
help from the tutorial "Modeling Nanopores to Sequencing DNA"

Cheers
Monika

On Tue, Aug 14, 2012 at 5:43 AM, Sean T Kigerl <skigerl_at_ucsd.edu> 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 Hnanopore with a benzene ring) Any suggestions would be
> greatly appreciated!
>
> Sean Kigerl
>