VMD-L Mailing List

From: Basheer Subei (basheersubei_at_gmail.com)
Date: Fri Aug 15 2014 - 14:07:12 CDT

Thanks!

For reference, so what I did was print out the variable $num in
addIons.tcl, and plug that number into the Autoionize plugin
 in the "user-defined number of ions" option for K+ and Cl-. Of course, I
also chose KCl as the salt, and used sin_hex.psf and sin_hex.pdb as the
input files.

On Fri, Aug 15, 2014 at 1:54 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:

> Basheer,
> This part of the tutorial is outdated. You no longed need sod2pot. User
> Autoionize plugin instead.
> http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/
>
> Maxim
>
> On Aug 15, 2014, at 1:45 PM, Basheer Subei <basheersubei_at_gmail.com> wrote:
>
> 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
>
>
>