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    FloppyTail has a centroid phase, it is crashing because it can’t find a centroid residue type for the CA atom.

    If FloppyTail will not be remodeling the area with the calciums, then just delete them and don’t worry about it. Rosetta’s scorefunction isn’t going to handle the calciums well anyway. (I wouldn’t trust Rosetta to do it right, but I’m happy to explain how to give it a shot.)

    If it IS going to try to remodel that region, you’ll have to hack together a calcium centroid residue type, or add code to re-place the calciums after the centroid phase ends. If you want to add a calcium residue type, try this (these instructions are approximate, I’ve never done it):

    1)look in rosetta_database/chemical/residue_type_sets/fa_standard/residue_types
    2)find calcium, and copy it to chemical/residue_type_sets/centroid/residue_types; also add it to centroid/residues.txt
    3)find the calcium atom specification in chemical/atom_type_sets/fa_standard/???, and copy it to chemical/atom_type_sets/centroid/???, modifying it as necessary to match the other centroid atom types.