/usr/share/autodock/Tests/1pgp_smaller.dpf is in autodock-test 4.2.6-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | 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
quaternion0 0 0 0 1 # initial quaternion
dihe0 0 0 0 0 0 0 0 0 0 0 0 # initial dihedrals (relative) or random
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
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
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