VMD-L Mailing List

From: Basheer Subei (basheersubei_at_gmail.com)
Date: Fri Aug 15 2014 - 13:45:20 CDT

Hello,

I just noticed that VMD 1.9 recently dropped
<http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/devel.html> the Autoi:sod2pot
function, and that creates a problem for users following along with the
"Modeling Nanopores for Sequencing DNA" tutorial
<http://bionano.physics.illinois.edu/Tutorials/nanopore-protocols.pdf>.

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