On Thu, May 21, 2015 at 11:10 AM, Emilia C. Arturo (Emily) <eca38@drexel.edu> wrote:
Yes, you're absolutely right, and I hadn't found documentation for phenix.metal_coordination to help me gauge whether 'my' irons were like those used to inform how phenix generated the edits file. Do you happen to know on what the tool bases its ideal distances? 

There are taken from a literature survey some time ago.
 

Do you have any references you can share that discuss how Fe-ligand distances change with charge and spin state, whether its observable in crystal structures or solution? Or, maybe you can suggest search terms to help me out as I am quite naive about bio-inorganic chemistry?

A more recent survey could possibly be of help to you but you have data that may be telling you what you need to do. You can also add a slack option to the edit which makes the potential well flat bottomed. If you made it say 0.2 then the metal coordinate would be very flexible and you wouldn't have the nonbonded term pushing them apart.


Cheers

Nigel

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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
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