From: Michael Robinson (
Date: Tue Mar 03 2020 - 23:57:34 CST

Hi All,

I've been looking into simulating large, nucleic-acid based systems in
recent weeks. The standard VMD ionization procedure doesn't seem
appropriate in these cases, due to the highly localized nature of the ion
placement required - thus my experimenting with cionize. For reference, my
current setup uses a .tcl script that is called alongside VMD:

package require cionize
namespace import ::cionize::*

mol load pqr test.pqr

cionize -mol 0 -mg -prefix test -np 16 -ions "{SOD 7947 1}"

While this does generate the desired ion placement, it outputs these ions
in a separate .pdf file. Given the complexity of my system, regenerating
the .pdb and .psf file of the original system with ions added isn't
trivial, and it seems like there must be an option I'm missing that outputs
a combined .pqr with both the contents of the original .pqr file and the
ions generated. I've tried to look through the code for cionize, but I have
to admit I'm coming up blank here.

Is the intended functionality of cionize to output as a separate .pdb file,
and then psfgen is used to regenerate the .psf file with the ions included?
Are there any alternatives to this approach?

Thank you for any help you can offer,