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    After you build the applications by issuing ./ -jN mode=release bin from the rosetta directory, you should find all of the executables in the rosetta/bin directory. The executables generally have descriptive names. To run docking, execute the “docking_protocol.[OS_TYPE][COMPILER][MODE]” (e.g. docking_protocol.linuxgccrelease) executable. The documentation pages should provide you with commonly used flags to give you additional guidance you need. The documentation for docking can be found here: