From: Jeff Comer (
Date: Sat Aug 23 2014 - 12:43:41 CDT

Hi Basheer,

Using the already

Jeffrey Comer, PhD
Assistant Professor
Department of Anatomy and Physiology
Kansas State University
College of Veterinary Medicine

On Fri, Aug 22, 2014 at 7:35 PM, Basheer Subei <> wrote:
> Hello all,
> In the Nanopore Tutorial (forgive me if this is the wrong mailing list), in
> section 3.6, the first step is to combine both the SiN nanopore and the
> dsDNA by running the script "combine.tcl. However, the script uses the
> unequilibrated structures "dsdna.pdb" and "sin_pore_charges.pdb" (i.e.
> before minimization and equilibration).
> Is there a reason why the tutorial doesn't just use the already-equilibrated
> structures from the previous sections 3.1 and 3.3? I just want to make sure
> that there isn't some reason unknown to me why I can't just use the
> equilibrated dsDNA and SiN nanopore and combine them. (of course, I'll take
> care to remove the water and ions from the DNA before combining it with the
> nanopore and then minimize and equilibrate the combined system as normal)
> Am I on the right track? Thanks in advance!
> - Basheer Subei
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