From: Basheer Subei (
Date: Fri Aug 15 2014 - 13:45:20 CDT


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

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

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