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    I assume you’re running the test provided in the test/integration/tests/enzdes directory. (The path you provided got cut off.)
    What you probably want to do is copy that entire directory as-is to a convenient location. Then you would change directories into that copied directory, and while in that directory, run your “/usr/local/rosetta3.2/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ @flags > enzdes.log”

    Note that there is an “inputs” subdirectory. You want to keep it as a subdirectory, as the flags file, as written, specifies a relative path to the files (if you look at the flags file you’ll see the “inputs/…” designation of files. — Note that you can put all the files into a single directory, but you’ll have to change the flags file to refer to the correct location.