used 1kv2 and ligands that I have setup from the PDBBIND
** will want to get more protein complexes--run this through relax or something.

Generate Conformers
bcl.exe molecule:ConformerGenerator -rotamer_library csd -top_models 100 -ensemble_filenames 1KV2_Validation_Affinities_3D.sdf -conformers_single_file 1KV2_Validation_Affinities_3D_conf.sdf -conformation_comparer 'Dihedral(method=Max)' 30 -max_iterations 1000
(If the bcl.exe does not work, make sure you are in the meilerlab environment: type "sbset meilerlab").



python /programs/x86_64-linux/rosetta/3.9/tools/hts_tools/sdf_split_organize.py starting_files/1KV2_Validation_Affinities_3D.sdf split_ligands/ ligand_names.csv

/programs/x86_64-linux/rosetta/3.9/tools/hts_tools/setup_screening_project.py ligand_names.csv ligand_db.db3

<< some editing done to the ligand_activitites file>>
echo "ligand_id,tag,value" >> ligand_activities.csv
echo "string,string,float" >> ligand_activities.csv
for ligands_list in ` awk -F ',' '{print $1}' ./ligand_names.csv | tail -n+3 `; do  for proteins_list in `ls ../protein_files/1KV2_cleaned_000*`; do  echo "${ligands_list},${proteins_list},1.0" >> ligand_activities.csv ; done done
In your favorite text editor, find and replace "../protein_files/".

python2.7 /programs/x86_64-linux/rosetta/3.9/tools/hts_tools/add_activity_tags_to_database.py ligand_db.db3 ligand_activities.csv
python2.7 /programs/x86_64-linux/rosetta/3.9/tools/hts_tools/make_params.py -j 2 --database /programs/x86_64-linux/rosetta/3.9/main/database/ --path_to_params /programs/x86_64-linux/rosetta/3.9/main/source/scripts/python/public/molfile_to_params.py ligand_db.db3 params/
ls params/*/* to see all the files you just created. I would highly suggest walking through one of these params files while looking at the corresponding PDB structure in a graphics program (pymol, chimera, MOE, your favorite).

/programs/x86_64-linux/biopython/1.65/bin/python /programs/x86_64-linux/rosetta/3.9/tools/hts_tools/make_evenly_grouped_jobs.py params/ protein_files/ --n_chunks 1 --max_per_job 1000 job

/programs/x86_64-linux/rosetta/3.9/main/source/bin/rosetta_scripts.default.linuxgccrelease @ flags.txt -in:file:screening_job_file job_01.js -parser:protocol dock.xml -out:path:all output_files
