autodock_parameter_version 4.1       # used by autodock to validate parameter set
outlev 0
parameter_file AD4.1_bound.dat       # New parameter library
#include_1_4_interactions 1.0        # test
intelec                              # calculate internal electrostatic energy

seed 28641 1106107140                # seeds for random generator

ligand_types C HD OA P               # ligand atom type names
fld 1pgp_rec.maps.fld                # grid_data_file
map 1pgp_rec.C.map                   # atom-specific affinity map
map 1pgp_rec.HD.map                  # atom-specific affinity map
map 1pgp_rec.OA.map                  # atom-specific affinity map
map 1pgp_rec.P.map                   # atom-specific affinity map
elecmap 1pgp_rec.e.map               # electrostatics map
desolvmap 1pgp_rec.d.map             # desolvation map

move 1pgp_lig.pdbqt                  # small molecule
about 22.894 28.598 40.259           # small molecule center
tran0 22.894 28.598 40.259           # small molecule center
quat0 1 0 0 0                        # initial quaternion
dihe0 0 0 0 0 0 0 0 0 0 0 0          # initial dihedrals (relative) or random
tstep 0.0                            # translation step/A
qstep 0.0                            # quaternion step/deg
dstep 0.0                            # torsion step/deg
unbound 0.0                          # free energy of the unbound state

rmstol 2.0                           # cluster_tolerance/A
epdb                                 # compute energy of PDBQT specified by 'move' 

extnrg 1000.0                        # external grid energy
e0max 0.0 10000                      # max initial ernergy; max number of retries

ga_pop_size 150                      # number of individuals in population
ga_num_evals 250                     # maximum number of energy evaluations
ga_num_generations 4                 # maximum number of generations
ga_elitism 1                         # number of top individuals to survive to next generation
ga_mutation_rate 0.02                # rate of gene mutation
ga_crossover_rate 0.8                # rate of crossover
ga_window_size 10                    # 
ga_cauchy_alpha 0.0                  # Alpha parameter of Cauchy distribution
ga_cauchy_beta 1.0                   # Beta parameter Cauchy distribution
set_ga                               # set the above parameters for GA or LGA

sw_max_its 30                        # iterations of Solis & Wets local search
sw_max_succ 2                        # consecutive successes before changing rho
sw_max_fail 2                        # consecutive failures before changing rho
sw_rho 1.0                           # size of local search space to sample
sw_lb_rho 0.01                       # lower bound on rho
ls_search_freq 0.06                  # probability of performing local search on individual
set_psw1                             # set the above pseudo-Solis & Wets parameters

ga_run 1                             # do this many hybrid GA-LS runs

analysis
