First off, I believe that UNK is special cased in Rosetta. I wouldn’t use it as a three letter code. Pick some other combination of three letters instead.
But on your main issue, my guess is that you edited your params file, and in the ATOM lines where you saw “X” you changed it to “W”. That “X” wasn’t the chain letter (the chain letter does not appear at all in the params file), it was the MM AtomType designation. (“X” simply means “unspecified” — that’s fine, as for regular ligand docking you never need to consult the MM AtomType designation.) If you leave it as “X”, that should fix the error you’re getting.
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