On Thu, Jun 06, 2013, venkatesh s wrote:
>
> i am struggling with iron-sulfur cluster parametrization
> Unknown residue: SF4 number: 0 type: Terminal/last
This is a difficult problem: iron sulfur cubane clusters come in three
oxidation states, and reliable vibrational spectra have only recently become
available. One not only needs parameters for FS4, but also revised parameters
for the four CYS residues that are connects to the iron-sulfur cubane.
We are working to prepare a set of files that will allow such active sites to
be modeled, but this is still a work in progress, and more testing is needed.
Some CHARMM force field parameters for the 2- state are discussed by Mitra
et al. Biochemistry 50:5220, 2011. These may help, but you will need to know
a lot about force fields and how they are represented in Amber parameter
files. It's not just a matter of loading a PDB file.
...regards...dac
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Received on Wed Jun 05 2013 - 13:00:03 PDT
