From: João Ribeiro (
Date: Fri Apr 20 2018 - 12:57:04 CDT

Hi Olga,

The are two possible reasons for your Zn ions to disappear: the first is
that the Input PSF and PDB entries were not updated in the Autoionizr GUI
(not the top molecule in VMD), and the other is that you used the same
"Segment name of placed ions" in the Autoionize Gui. I would say that the
latter is the most probable reason. Try to assign different segment names
when placing the ZN ions and the NaCl salt concentration and all the ions
should be in the final structure.



On Fri, Apr 20, 2018 at 12:33 PM, Olya Kravchenko <> wrote:

> Hi all,
> my system is a protein + one or several Zn ions in a water cube, I want to
> add NaCl and set different concentrations of NaCl, say 0.15 and 0.5 for two
> separate systems.I use autoionize plugin for that. I place Zn ions first,
> save it, then take the pdb/psf files containing protein + Zn ions in a
> water cube and autoionize it using option "Neutralize and set concentration
> of NaCl to 0.15mol/L". This erases my Zn ions! Am I missing something
> simple?
> Thanks!!
> Olga

João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
+1 (217) 3005851