Quick question: I’ve noticed that some of the .params files in residue_types/metal_ions have a “formal charge entry” such as for Zn: CHARGE ZN FORMAL +2, but some other divalent cations like Co lack this entry.
Is this entry even used by Rosetta?
Could some of these entries be incorrect?
Should the formal charge entry be added if I want to use that metal ion?
The formal charge setting in the params file is not used by regular Rosetta applications. It’s currently only used by the Gasteiger atom typing machinery, which is itself is not really used by anything at the moment, apart from a few experimental protocols. These entries therefore could indeed be incorrect, and it might be that some of the params files are currently missing them. You can add them if you want, but it shouldn’t affect anything.
For charges, it’s the partial charge value at the end of the ATOM line in the params file which is used for the Coulombic calculation of fa_elec. These should be set appropriately to give you good results in standard scoring.