AMBER Archive (2009)

Subject: [AMBER] Fe and Mn simulations

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Tue Jun 30 2009 - 15:22:14 CDT

Hi Amber users/developers,

We are studying a Fe/Mn binding protein using MD simulations.
Initially, I was guessing what changes in protein mobility one could
expect by changing the metal bound in the protein. For such purpose, I
was guessing how to setup such a system and would like to hear
specialists opinion about that.
Metal is bound to a 3His/1Asp/1WAT residues

* Is this a case for a QM/MM study our can MM alone provide an
realistic model for the system?
* Can you guys point me to some papers regarding the subject?
* To someone who has never parametrized metals, which method would be
suitable for metal parametrization (for MM simulations)? Any
suggestion about charge method, theory level, basis set...

Thanks a lot in advance, 

--
[ ]s

--Alessandro S. Nascimento
University of Sao Paulo
Biomolecular Physics

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