These are Amber force field files for iron-sulfur cubane systems in the -1
(HIPIP), -2 (Fdox), and -3 (Fdred) oxidation states.  The intent is that
the cubane be coordinated by four CYF residues (deprotoned CYS residues).

There are two sets of cubane off files: in the (old) version 2 of the
PDB, this component was called FS4; in more recent (version 3) files, it
is called SF4.  The only difference between the FS4*.off and the
SF4*.off files is in this naming convention:  use the files that match
the PDB input you have.  CYF files are also provided for each of the three
oxidation states; use SF4pm1.off with CYFpm1.off, etc.

The force field fits were based on quantum calculations reported here:

Y. Xiao, M. Koutmos, D.A. Case, D. Coucouvanis, H. Wang and
S.P. Cramer. Dynamics of an [Fe_{4}S_{4}(SPh)_{4}]^{2-} cluster
via IR, Raman, and nuclear resonant vibrational spectroscopy
(NRVS). Analysis using ^{36}S substitution, DFT and empirical force
fields. J. Chem. Soc. Dalton, 2192-2201 (2006)

The charges were derived from the electrostatic potentials; bonded
parameters by requiring that the normal modes arising from the force
field match those from the quantum calculations.

There are sample tleap inputs to show how these could be used to set up
Amber simulations.  Note that there is certainly no guarantee that
precise differences between cubanes in different oxidation states will
be reproduced by the force fields described here.

Force fields were created in 2012 by Steve Sontum and David Case.  In
the way of the world, they were never published....

A similar approach, with a different method for getting bonded
parameters is reported here:

A.T.P. Carvalho and M. Swart.  Electronic Structure Investigation and
Parametrization of Biologically Relevant Iron-Sulfur Clusters.  J. Chem.
Inf. Model.  54: 613-620 (2014).
