VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Mon Apr 25 2016 - 14:25:32 CDT

Hi Afshar,

thank you for replying! I added another entry for Fe into autoionize plugin.

in case, somebody ever needs this: the easiest way to ionize the
system with non-supported ions such as Fe(II) is to ionize it with
another type of ions (such as Mg or Zn) and then change mass entry in
the newly created psf file for mass of Fe. Then edit parameter file,
i.e. change L-J parameters of the ion used to create psf to the ones
corresponding to Fe.

Olga

On Thu, Apr 21, 2016 at 6:07 AM, Ashar Malik <asharjm_at_gmail.com> wrote:
> 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
>
> /plugins/noarch/tcl/autoionize1.3
>
> 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 <ovkrav_at_gmail.com> 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
>>
>
>
>
> --
> Best,
> /A