Commands used in bash: rosetta_bin '=' Path to binary # run with Angle constraints: $rosetta_bin/docking_protocol.static.linuxgccrelease -in:file:s pose_0_0.pdb -unboundrot pose_0_0.pdb @flagDockingwConstr # flagDockingwConstr: -nstruct 10 -partners A_B -dock_pert 3 8 -ex1 -ex2aro -constraints:cst_file AngConstraint.cst -constraints:cst_weight 100 -out::prefix docked_ -overwrite # run with Distance constraints: $rosetta_bin/docking_protocol.static.linuxgccrelease -in:file:s pose_0_0.pdb -unboundrot pose_0_0.pdb @flagDockingwDistConstr -nstruct 10 -partners A_B -dock_pert 3 8 -ex1 -ex2aro -constraints:cst_file DistConstraint.cst -constraints:cst_weight 100 -out::prefix docked_ -overwrite # run with cst_fa_file flag and Angle constraints (crashes) $rosetta_bin/docking_protocol.static.linuxgccrelease -in:file:s pose_0_0.pdb -unboundrot pose_0_0.pdb @flagDockingwConstr_err # flagDockingwConstr_err: -nstruct 10 -partners A_B -dock_pert 3 8 -ex1 -ex2aro -constraints:cst_fa_file AngConstraint.cst -constraints:cst_weight 100 -out::prefix docked_ -overwrite # AngConstraint.cst Angle N 39A CA 14A CA 14B FLAT_HARMONIC 1.57 0.1 0.0175 Angle CA 14B N 39B N 39A FLAT_HARMONIC 1.57 0.1 0.0175 Dihedral CA 14A CA 14B N 39B N 39A FLAT_HARMONIC 0 0.1 0.0175 # DistConstraint.cst AtomPair CA 71A CA 62B HARMONIC 7.0 0.1