flags_for_rosetta_ab_initio

-in:file:fasta PATH_TO_QUERY_SEQUENCE_FILE 
-in:file:frag3 PATH_TO_THREE_RESIDUE_FRAGMENTS_FIE
-in:file:frag9 PATH_TO_NINE_RESIDUE_FRAGMENTS_FILE

-abinitio:relax
-nstruct 100

-out:pdb
-out:overwrite

-database PATH_TO_ROSETTA_DATABASE_DIRECTORY

-cst_fa_file PATH_TO_CONSTRAINT_FILE
-use_filters true
-psipred_ss2 PATH_TO_SECONDARY_STRUCTURE_PREDICTION_FILE
-abinitio::increase_cycles 20
-abinitio::rg_reweight 0.5
-abinitio::rsd_wt_helix 0.5
-abinitio::rsd_wt_loop 0.5

-constraints:cst_weight 0.5
-constraints:cst_fa_weight 0.5