config_plants_speed1.txt

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# All parameters are set to default
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# SEARCH ALGORITHM
search_speed speed1              # speed1 (highes realibility) speed2 speed4 (higer speed, low realibility)

# aco_ants  20                  # number of ants (standard: 20)
# aco_evap  0.5                 # evaporation factor [0; 1]
# aco_sigma  2.3                # iteration scaling factor

# flip_amide_bonds 0              # activate (1) or deactivate ipping of amide bonds (standard:0)
# flip_planar_n 1                 # activate (1) or deactivate flipping of bonds next to planar nitrogens (standard: 1)
# force_flipped_bonds_planarity 0 # activate (1) or deactivate (0) automatic planarity correction for  flippable bonds (standard: 0)
# force_planar_bond_rotation 1    # activate (1) or deactivate (0) free rotation of planar bonds (standard: 1) rescore mode value: perform simplex optimization during rescoring (value=simplex) or only direct input conformation scoring (value=no simplex) (standard: simplex)
# flip_ring_corners 0             # activate (1) or deactivate flipping of free ring corners (standard: 0)

# BINDING SITE 
bindingsite_center 62.21 5.02 -23.68 
bindingsite_radius 17.83

# CLUSTER ALGORITHM
cluster_rmsd 2.0                 # RMSD similarity threshold for cluster algorithm (standard:2.0)
cluster_structures 10            # number of structures generated by the cluster algorithm (standard: 10)

# SCORING FUNCTION
 # Intermolecular
# scoring_function chemplp            # plp, plp95 or chemplp (standard: chemplp)
# outside_binding_site_penalty 50.0   # scoring functions using precalculated grids use value to fill grid points outside the binding site definition (standard: 50.0)
# enable_sulphur_acceptors 0          # activate (1) or deactivate (0) scoring of sulphur acceptors (standard: 0)
 # Intramolecular
# ligand_intra_score clash2                 # [clash, clash2] (simple heavy-atom clash terms) or lj (all-atom Lennard-Jones term) (standard: clash2)
# chemplp_clash_include_14 1                # activate (1) or deactivate (0) scoring of 1-4 interactions (standard: 1)
# chemplp_clash_include_HH 0                # activate (1) or deactivate (0) scoring of hydrogenhydrogen interactions (standard: 0)

# missing Keywords affecting scoring function plp, plp95 and chemplp

# INPUT OPTIONS (no gold input allowed)
# protein_file rec_2.pdbqt                 # protein filename
# ligand_file lig.pdbqt                    # ligand filename
# ligand_list ligands.txt                  # text file containing ligand filenames

# OUTPUT OPTIONS 
output_dir /folder/out                 # name of output directory; PLANTS automatically tries to create a subdirectory with the specified name and exits if the directory already exists to prevent overwriting existing data

# FLEXIBLE SIDE-CHAINS (reccomended flexible_protein_side_chain)

# flexible_protein_side_chain VAL123,VAL123  # string: residue label of flexible side-chain (e.g. VAL123)
# flexible_protein_side_chain 100            # value: residue number of flexible side-chain (e.g. 100 )
# intra_protein_score_weight 0.6             # weighting factor for the intramolecular protein score (standard: 0.6)
# fix_protein_bond value                     # keep protein bond with bond-number value fixed.