-run -constant_seed -jran 123456 -in -file -s protein_relA_FDA.pdb -extra_res_fa LG1.params -extra_res_fa LG2.params -path -database /software/linuxsoft/rosetta-3.5/rosetta_database -out -file::silent sil1.out -packing -no_optH -ex1 -ex1aro -ex2 -parser -protocol fda_dock.xml -mute core.util.prof ## dont show timing info -mute core.io.database