1. Generate conformers with the BCL

bcl.exe molecule:ConformerGenerator -ensemble_filenames INPUT.sdf -conformers_single_file OUTPUT.sdf

2. For the options menu of the BCL conformer generator

bcl.exe molecule:ConformerGenerator -help

3. Generate Rosetta params file from SDF input

/PATH-TO-ROSETTA/main/source/scripts/python/public/molfile_to_params.py INPUT.sdf --name=THREELETTERCODE --chain=ONELETTERCODE --conformers-in-one-file

4. Generate a single set of Rosetta models

/PATH-TO-ROSETTA/main/source/bin/rosetta_scripts.linuxgccrelease @inputs/options -docking:ligand:ligand_ensemble 0 -nstruct 1
