/usr/share/autodock/Tests/1pgp_flexres.dpf is in autodock-test 4.2.6-3.
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 | autodock_parameter_version 4.2 # used by autodock to validate parameter set
outlev 0 # diagnostic output level
intelec # calculate internal electrostatics
seed 28641 1106107140 # seeds for random generator
ligand_types P C HD OA N # atoms types in ligand
fld 1pgp_rigid.maps.fld # grid_data_file
map 1pgp_rigid.P.map # atom-specific affinity map
map 1pgp_rigid.C.map # atom-specific affinity map
map 1pgp_rigid.HD.map # atom-specific affinity map
map 1pgp_rigid.OA.map # atom-specific affinity map
map 1pgp_rigid.N.map # atom-specific affinity map
elecmap 1pgp_rigid.e.map # electrostatics map
desolvmap 1pgp_rigid.d.map # desolvation map
move 1pgp_lig.pdbqt # small molecule
flexres 1pgp_flex.pdbqt # file containing flexible residues
about 23.407 29.2817 39.8079 # small molecule center
tran0 23.407 29.2817 39.8079 # initial coordinates/A or random
quaternion0 0 0 0 1 # initial quaternion
dihe0 0 0 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
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 energy; 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
unbound_model bound # state of unbound ligand
ga_run 1 # do this many hybrid GA-LS runs
analysis # perform a ranked cluster analysis
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