I am a beginner in Rosetta and I am wondering if Rosetta could do ab initio folding of a metalloprotein with multiple metal ions.
I read the article by Wang et al.,(Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry, 2010, Protein Science) and was able to set constraints for one metal binding site in residue_pair_jump_cst file and run AbinitioRelax without any issues. However I have no idea how to set things up when two or more metal ions are involved. Do I also have to define every jump between those metal ions?
I would be grateful if someone could help.