VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Wed Apr 20 2016 - 15:01:39 CDT

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