| # 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 | |