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    Maybe Rosetta thinks it’s the best rotamer. Does it says “generating X rotamers at Y positions” or something similar?

    I believe if it’s a phospholysine, you should be able to convince Rosetta to use the existing lysine rotamer library instead of having to create your own. If you WANT to create your own, I’ll put you in contact with someone who’s good at it.

    Did you create a phospholysine residue type, or did you modify one of the phosphorylation patches to apply to lysine?