Backrub step command line example:

rosetta_scripts.linuxgccrelease
-parser:protocol flex_ddG-backrub_step.xml
-s wt_pdb_path # Starting WT crystal structure
-in:file:fullatom
-parser:script_vars
mutate_resfile_relpath=%s # Path to a resfile specifying mutant positions. Can be any set of mutations (only the positions matter), as mutations are made in the next step. Positions need to be known now to pick backrub region.
backrub_kt=1.2
backrub_trials=36000
backrub_stride=12000
neighbor_distance=12.0
sc_sample_rotwells_unif=0
min_tolerance=0.000001
min_max_iter=5000
min_abs_score_convergence_threshold=1.0

Mutation step command line example:

rosetta_scripts.linuxgccrelease
-parser:protocol flex_ddG-mutation_step.xml
-s wt_minimized_pdb_path # Path to the WT minimized PDB structure from the first script, needed to score ddG calculation
-native # Path to the starting WT crystal structure, needed so that same neighbor residue bubble is selected
-in:file:fullatom
-parser:script_vars
chainstomove=%s
mutate_resfile_relpath=%s # Path to resfile specifying mutations
min_tolerance=0.000001
min_max_iter=5000
neighbor_distance=12.0
min_abs_score_convergence_threshold=1.0
backrub_pdb_path=%s # Path to backrub PDB output from earlier step, mutations will be applied to this model