AMBER Archive (2008)

Subject: AMBER: Polarizable force field for divalent ions?

From: Yi-Ming Cheng (d90223013_at_ntu.edu.tw)
Date: Wed Jul 23 2008 - 05:59:08 CDT

Dear all,
   I'm facing a problem about how to generate a polarizable force
field for divalent ions. My simulation system is comprised of a small
peptide with a divalent ion, i.e. zinc or iron. (Not zinc finger
protein) I was suggested to use a polarizable force field for both of
the peptide and ion to get a reliable result since the ion is not
fixed to a position nearby the peptide. Ideally, the ion should be
able to move around the peptide and forms a dynamic equilibrium
between docked-to-peptide and undocked states. Unfortunately, as far
as I know, the only polarizable force field provided with AMBER
package is ff02, which does not support these ions. So, my question is
that would it be possible to generate a polarizable force field for
divalent ions? Any suggestions about literatures or any ideas would be
largely appreciated. Thank you.
Yi-Ming Cheng

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