From: Ashar Malik (
Date: Thu Apr 21 2016 - 05:07:04 CDT

Regarding the first option you discuss, you can look up magnesium in the
topology file and change all of the definitions in it and for the
parameters of that in the parameter file to that of Fe2+ or Fe3+. Leave the
name label the same -- and what will happen is that it would read Mg in the
PDB and PSF files but it would actually be iron instead. I would not
recommend this method though since some systems have Magnesium and with the
above approach those would become Fe as well (as far as the topology and
parameters are concerned).

The appropriate way (at least what I think is appropriate) is to tweak the
plugin. The code(s) can be reached in your install directory in


you should be able to make the additions fairly easily (I think -- as the
code has comments) so that along with the default ions it recognizes iron
as well.

Caution: Iron is a transition metal. Parameters for transition metals are
questionable. Ionizing a big system (like the one from your previous post)
with the likes of iron is maybe not the best thing to do. So be careful if
you must ionize with a transition metal.

On Thu, Apr 21, 2016 at 8:01 AM, Olya Kravchenko <> wrote:

> Hi all,
> I would like to add free Fe(II) ions to my system (which is a solvated
> ferritin molecule). Since autoionize does not support Fe I thought
> about modifying parameters for one of the supported ions (for example,
> Mg) and use it as a substitute for Fe while running autoionize. If I
> were to do this, where would I make this modification, i.e. how do I
> access parameters that autoionize refers to? Or is there another way
> to call for my own modified topology/parameters files while using
> autoionize?
> If anyone had to add free Fe ions into the system, is that how you did
> it, or is there another way?
> Thanks!
> Olga