File size: 2,558 Bytes
35aaa09 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 | # 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
|