From: Maxim Belkin (
Date: Fri Aug 15 2014 - 13:54:08 CDT

This part of the tutorial is outdated. You no longed need sod2pot. User Autoionize plugin instead.


On Aug 15, 2014, at 1:45 PM, Basheer Subei <> wrote:

> Hello,
> I just noticed that VMD 1.9 recently dropped the Autoi:sod2pot function, and that creates a problem for users following along with the "Modeling Nanopores for Sequencing DNA" tutorial.
> In section 3.3.11 in that tutorial, it instructs users to run the addIons.tcl script, which adds KCl ions. The last line of addIons.tcl reads "Autoi::sod2pot".
> What should users of VMD 1.9+ do about Autoi::sod2pot being removed? Does this affect the tutorial? (I'm assuming it does, because then it wouldn't convert the sodium ions into potassium ions). What should I use instead of sod2pot?
> If someone could help here (and perhaps fix the tutorial as well), that would be great! I would also gladly accept links to the documentation of Autoionize (which I couldn't find).
> Thank you for your time!
> - Basheer Subei