Ideally, Rosetta should give a sensible error message rather than just dieing like that, but segmentation faults generally mean that your system/input files have something about them that the original developers didn’t anticipate (but should have).
The best way to trouble shoot them is to compile and run in debug-mode. To compile in debug mode, just leave the “mode=release” off of the scons command (something like “scons -j8 bin/docking_protocol.linuxgccdebug”). To run the debug mode build, use the docking_protocol.linuxgccdebug executable instead of the docking_protocol.linuxgccrelease one.
Debug mode runs much slower than release because it’s performing additional checks. Occasionally the debug build by itself will be helpful, but frequently you need to run under a debugger like gdb. To do so, just run “gdb /usr/local/rosetta3.2/rosetta_source/bin/docking_protocol.linuxgccdebug” on the normal command line, and then do a “run -database /usr/local/rosetta3.2/rosetta_database/ -s input1.pdb -dock_ppk” on the gdb command line. After a long while, it’ll stop with an error message. You can then run “bt” (“backtrace”) to get detailed information on where the program stopped. Usually the error message and the backtrace should be enough to figure out what the problem is. (So you can then quit gdb with the “quit” command.)