I am working with an enzyme that uses Fe4S4 iron-sulfur clusters as co-factors. I recently built a model (using other software) and want to use ROSETTA for optimisation and enzyme design. I am very new to the software suite, and have managed to relax the protein together with the substrate ligand, for which I have a mol2 file. I would also like to include the iron-sulfur cluster, for which I have PDB coordinates, as well as AMBER PREP and FRCMOD files.
Is there a way of incorporating the cluster, and if so, how do I do this? The cluster is coordinated by cysteines - how do I tell the program to bond the CYS residues to the cluster?
Secondly, I have a second iron-sulfur cluster in the enzyme for which there is only PDB coordinates (no parameters). How would I go about incorporating this cluster?
I am very new to the ROSETTA suite, and any help is greatly appreciated.