
-in
 -path
  ## On a large cluster, the database should be on a local scratch disk
  ## to avoid over-taxing NFS.
  #-database /scratch/USERS/davis/minirosetta_database
  ## "Fallback" database locations can also be specified,
  ## in case the primary database is missing on some nodes:
  #-database /work/davis/minirosetta_database
  ## Location provided by user:
  #-database /work/nivon/install/minirosetta_database
 -file
  ## You must supply .params files for any residue types (ligands)
  ## that are not present in the standard Rosetta database.
  ## Centroid residues are not needed for docking,
  ## but may be needed for other Rosetta protocols.
  #-extra_res_cen ligand/cen/CP1.cen.params
  -extra_res_fa inputs/CP1.fa.params
  -s inputs/7cpa_no_ligand_CP1_silent.out 
  -tags 7cpa_no_ligand_CP1_0_0012
-out
 ## These channels generate a LOT of output,
 ## especially with -improve_orientation.
 -mute protocols.geometry.RB_geometry core.scoring.dunbrack.SingleLigandRotamerLibrary core.scoring.rms_util
 -file
  ## I prefer output structures with Rosetta numbering, from 1 to N residues.
  ## To keep the original PDB numbering, omit this flag:
  -renumber_pdb
-run
 ## Recording the SVN revision of the code in your output files
 ## makes it easier to figure out what you did later.
 -version
 ## MT is now the default random number generator, actually.
 #-rng mt19937
 ## Rosetta's default behavior is to pretend that atoms with zero occupancy
 ## don't exist at all, which can lead to whole residues disappearing...
 -trust_missing_coords
-packing
 ## Includes the input sidechain conformations as rotamers when repacking,
 ## but they can be "lost" if any other rotamer is chosen at that position.
 #-use_input_sc
 ## Instead, use -unboundrot to permanently add the rotamers from one or more
 ## PDB files.  Their rotamer ("Dunbrack") energies are also adjusted to be
 ## equal to the best rotamer at that position, thereby favoring the native.
 ## Since most sidechains do not change position much upon ligand binding,
 ## including this knowledge generally improves docking results:
 #-unboundrot ...
 ## Controls the number of (protein) rotamers used.
 -ex1
 -ex1aro
 -ex2
 ## Ensures that extra rotamers are used for surface residues too.
 -extrachi_cutoff 1
-docking
 -ligand
  ## Use soft-repulsive scoring during search (but not final minimization).
  ## This slightly improves search.  Hard-rep is used for final scoring,
  ## however, because it gives better discrimination.
  -soft_rep
  ## Like Rosetta++, only evaluate the Coloumb term between protein and ligand.
  -old_estat
