/software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/source/bin/enzyme_design.linuxgccrelease -s /home/qgem/Documents/dockedDomain2.pdb -resfile /home/qgem/Documents/positions.resfile -enzdes:cst_opt -enzdes:cst_design -enzdes:design_min_cycles 3 -enzdes:cst_min -packing:ex1 -packing:ex2 -packing:use_input_sc -packing:linmem_ig 10 -out::overwrite -out:path:pdb /home/qgem/Documents/pdbs -out:path:score /home/qgem/Documents/pdbs -o /home/qgem/Documents/output