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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 06 2009 - 12:23:12 PDT
