-nstruct 10
-in:ignore_unrecognized_res
-file:s cluster1_1_trim.pdb
-ex1
-ex2
-ex1aro::level 6
-ex2aro::level 6
-exdna::level 4
-use_input_sc
-run:output_hbond_info
-sparse_pdb_output
-out:path:score ./score_output/
-score:output_residue_energies
-adducts dna_major_groove_water
-out:path:pdb ./pdb_output/
-out:path:score ./score_output/
-score:weights dna
-out:levels all:warning protocols.dna:info protocols.multistate_design:info protocols.genetic_algorithm:info apps:info protocols.loops:info core.io.pdb:info
-jd2:dd_parser
-parser:protocol design.script
-out:prefix design_
-parser::output_schema rosettaDNA-output.xml