# AutoDock Configuration File
# Docking@HOME - Molecular Docking Parameters

# === Genetic Algorithm Parameters ===
ga_pop_size = 150                    # Population size for genetic algorithm
ga_num_evals = 2500000              # Maximum number of energy evaluations
ga_num_generations = 27000          # Maximum number of generations
ga_elitism = 1                      # Number of top individuals to survive
ga_mutation_rate = 0.02             # Rate of mutation
ga_crossover_rate = 0.8             # Rate of crossover
ga_window_size = 10                 # Window size for local search

# === Local Search Parameters ===
ls_search_freq = 0.06               # Probability of local search
sw_max_its = 300                    # Maximum iterations for Solis-Wets local search
sw_max_succ = 4                     # Maximum successes before changing rho
sw_max_fail = 4                     # Maximum failures before changing rho
sw_rho = 1.0                        # Initial step size for local search
sw_lb_rho = 0.01                    # Lower bound on rho

# === Docking Parameters ===
rmstol = 2.0                        # RMSD tolerance for clustering (Angstroms)
extnrg = 1000.0                     # External energy for atoms outside the grid
e0max = 0.0, 10000.0               # Maximum initial energy; max retries

# === Output Parameters ===
ga_run = 100                        # Number of docking runs
analysis = True                     # Perform cluster analysis

# === Grid Parameters ===
npts = 60, 60, 60                  # Number of grid points in x, y, z
gridfld = receptor.maps.fld        # Grid data field file
spacing = 0.375                     # Grid spacing in Angstroms

# === Flexibility Parameters ===
# torsdof = 14                      # Torsional degrees of freedom (calculated automatically)
about = 0.0, 0.0, 0.0              # Center of rotation for ligand

# === Energy Parameters ===
intelec = True                     # Calculate internal electrostatics
smooth = 0.5                       # Smoothing parameter

# === Simulation Parameters ===
seed = pid time                    # Random seed (pid time, or specify a number)
outlev = 1                         # Output level (0=minimal, 1=normal, 2=verbose)

# === Performance Parameters ===
# These are set automatically based on available resources
# Uncomment to override
# ga_num_threads = 4               # Number of CPU threads (if not using GPU)
# use_gpu = True                   # Use GPU acceleration if available