Re: [AMBER] Simulating protein with Fe atom

From: case <>
Date: Thu, 26 Dec 2013 09:55:59 -0500

On Wed, Dec 25, 2013, onetwo wrote:
> I have a protein which has a Fe at the active site, I want to do
> simulation. Fe is in co-ordination with one Asp residue, two histidines
> and one water molecule which plays a role in enzymatic activity.

Two good places to start: (a) Section 5.6 of the AmberTools manual (on "metal
center parameter builder"); (b) do a literature search to see how others have
handled metal centers like yours.

That said, iron is a very difficult metal to handle at the molecular mechanics
level, since it has both high- and low-spin forms for two common oxidation
states. A lot depends on what is going on, and what role the iron is playing.
You mention "enzymatic activity", which suggests that you might even need to
think about QM/MM models.

Bottom line: this appears to be a very advanced modeling challenge. Don't
think it will be easy, or that you will just get the "answer" on a mailing


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Received on Thu Dec 26 2013 - 07:00:05 PST
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