AMBER Archive (2007)

Subject: AMBER: query regarding parameter files for manganese

From: neetu_at_imtech.res.in
Date: Thu May 10 2007 - 07:43:44 CDT

> Dear all,
> I am new user of amber, so am seeking useful advice from you. My protein
is a metalloprotein containing Mn2+ ion coordinated to the following
ligand residues/ atoms:
Metal ion Ligand residue/atom distance (angstrom)
Mn1 His 58/ NE2 2.2
Mn1 His 60/ NE2 2.2
Mn1 Asp 315/ OD1 2.3
Mn1 Wat110 2.1
Mn2 Wat110 2.1
Mn2 His 183/ NE2 2.3
Mn2 His 239/ NE2 2.3
Mn2 Wat109 2.3
I need parameter files for manganese ion (Mn2+). Although, I have
parameters for non bonded interactions but will it be justified to use
them in this case as Mn2+ is bound through coordination bonds. If not
,then can somebody please guide me how to calculate parameters for
coordinate bonds.

> Thank you very much for your every suggestion,
  regards,

> Neetu Saxena
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