Options:
  
  --receptor_trim_dist FLOAT=5
                              Output receptor residues less than this distance from the docked ligand's pose (use with --output_docked_complexes)
  --probis_level FLOAT:FLOAT in [0 - 1]=0.9
                              The combined scoring function is a combination of two score terms, ProBiS-Score that relies on template ligands and GSscore, a general statistical scoring function: Combined-Score = h * ProBiS-Score + (1 - h) * GSscore
  --max_seq_id FLOAT=100      Upper bound for the sequence identity (%) of the proteins from which predicted (template) ligands are transposed by the ProBiS-Dock Database method - enables testing with excluded template ligands above certain seq. id.
  --max_frag_radius FLOAT=16  Maximum fragment radius for creating the initial rotamers
  --ref_state TEXT:{mean,cumulative}=mean
                              Normalization method for the reference state of the GSscore scoring function - 'mean' is averaged over all atom type pairs, whereas 'cumulative' is a summation for atom type pairs
  --comp TEXT:{reduced,complete}=reduced
                              Atom types used in calculating reference state 'reduced' or 'complete' in GSscore scoring function ('reduced' includes only those atom types present in the specified receptor and small molecule, whereas      'complete' includes all atom types)
  --rad_or_raw TEXT:{radial,normalized_frequency}=radial
                              Function for calculating scores 'radial' or 'normalized_frequency'
  --dist_cutoff FLOAT:FLOAT in [4 - 15]=6
                              Cutoff distance for the scoring function
  --step_non_bond FLOAT:FLOAT in [0 - 1]=0.01
                              Step for spline generation of non-bonded knowledge-based potential
  --scale_non_bond FLOAT:FLOAT in [0 - 1000]=10
                              Scale non-bonded forces and energy for knowledge-based potential
  --num_read_ligands INT=10   Maximum number of ligands to read in one chunk - set to higher values when reading from network disks
  --num_read_template_ligands INT=10
                              Maximum number of template ligands to read in one chunk
  --spin_degrees FLOAT:{5,10,15,20,30,60,90}=30
                              Spin degrees to rotate ligand
  --clash_coeff FLOAT=0.75    Clash coefficient for determining whether two atoms clash by eq. dist12 s< C * (vdw1 + vdw2)
  --tol_seed_dist FLOAT=2     Tolerance on seed distance in-between linking
  --lower_tol_seed_dist FLOAT=2
                              Lower tolerance on seed distance for getting initial conformations of docked fragments
  --upper_tol_seed_dist FLOAT=2
                              Upper tolerance on seed distance for getting initial conformations of docked fragments
  --max_possible_conf INT=200 Maximum number of possible docked conformations of compounds to generate (-1 = unlimited)
  --link_iter INT=10000       Maximum number of iterations for A-star linking of fragments back into molecules
  --docked_clus_rad FLOAT=0.75
                              Cluster radius between docked ligand conformations
  --max_allow_energy FLOAT=0  Maximum allowed energy for docked seed fragment conformations
  --iterative                 Enable iterative minimization during linking
  --n_cliques INT=100000      The number of maximum weight cliques with lowest energies to output
  --max_steps INT=100000000   Maximum number of steps the MCQDW algorithm is allowed (-1 = unlimited)
  --fftype TEXT:{kb,phy}=kb   Forcefield to use 'kb' (knowledge-based) or 'phy' (physics-based)
  --mini_tol FLOAT=0.0001     Minimization tolerance
  --max_iterations INT=100    Maximum iterations for minimization during linking
  --max_iterations_final INT=1000
                              Maximum iterations for final minimization
  --update_freq INT=200       Update non-bond list frequency in steps
  --position_tolerance FLOAT=1e-11
                              Position tolerance which tells when to stop minimization in Angstroms - only for kb
  --force_tol FLOAT=10000     Force convergence tolerance, conformations with unusually high forces after minimization will be discarded - only for kb
  --flex_radius FLOAT=8       Protein residues within this distance (in Angstroms) around the ligand will be flexible during minimization
  --top_percent FLOAT=0.15    Percent of top-scored docked seed fragment's poses to consider further for linking back into full molecule
  --k_clique_size INT=1000    To generate partial conformations of a docked molecule, this value represents the number of docked fragments required to be positioned in the binding site at distances with respect to each other, so that it is possible to reconstruct the original small molecule in the docked conformation. As a docked molecule typically consists of several fragments, the default large value indicates that the k-clique size to be searched will always be equal to the number of fragments in the docked molecule
  
  --grid_spacing FLOAT=0.75   Binding site grid resolution in Angstroms
  --num_univec INT=256        Number of unit vectors evenly distributed on a sphere for fragment conformation generation
  --conf_spin FLOAT=10        Spin degrees for fragment conformation generation
  --excluded_radius FLOAT=0.8 Excluded radius in Angstroms
  --max_interatomic_distance FLOAT=8
                              Maximum interatomic distance in Angstroms
  --dist_cutoff_probis_template FLOAT=1
                              Distance cutoff for ProBiS-Score scoring function in Angstroms
  --pow_probis_template FLOAT=1
                              How fast the template ProBiS-Score decays with distance from template atoms 1/(d+1)^pow
  --clus_rad FLOAT=2          Cluster radius for rigidly docked seeds in Angstroms
   --only_ligand_flexible      Only ligand is flexible (by default both ligand and receptor are flexible)