If you just want to compile fixbb, ligrpkmin, and liganddock, then you would do something like the following:
scons mode=release bin/fixbb.linuxgccrelease bin/ligrpkmin.linuxgccrelease bin/liganddock.linuxgccrelease
(Substitute the platform and compiler as appropriate)
The executable file will be in the rosetta_source/bin directory.
Regarding MPI, adding extras=mpi to the scons commandline should be enough, but you may need to alter your environment variables, etc. to make sure that your MPI compiler and libraries can be found when building.
.
