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    Warning: Unable to locate database file chemical/residue_type_sets/centroid

    ERROR: Unable to open file: ./chemical/residue_type_sets/centroid/residue_types.txt”

    You forgot to pass the -database flag.

    Loop modeling does not run under JD2 and thus doesn’t use MPI in the standard fashion. I am fairly, but not 100%, certain that it is MPI compatible anyway, it just doesn’t use the same flags, etc. I don’t think it has any MPI “options” at all – it’s either MPI or not.