ligandlgasw2.CARB.dpf Page 1 of 2
seed time pid # for random number generator types CNOHX # atom type names
fld proteinhx.CARB.fld # grid data file
map proteinhx.CARB.C.map # C-atomic affinity map file map proteinhx.CARB.N.map # N-atomic affinity map file map proteinhx.CARB.O.map # O-atomic affinity map file map proteinhx.CARB.H.map # H-atomic affinity map file map proteinhx.CARB.X.map # X-atomic affinity map file map proteinhx.CARB.e.map # electrostatics map file
move ligandhx.t.pdbqs # small molecule file about 33.432 19.380 9.418 # small molecule center
# Initial Translation, Quaternion and Torsions
tran0 33.432 19.380 9.418 # initial coordinates/A or "random" quat0 1. 0. 0. 0. # initial quaternion or "random" ndihe 5 # number of initial torsions
dihe0 0. 0. 0. 0. 0. # initial torsions
torsdof 1 0.0497 # num. non-Hydrogen torsional DOF & coeff.
# Initial Translation, Quaternion and Torsion Step Sizes and Reduction Factors tstep 2.0 # translation step/A
qstep 50.0 # quaternion step/deg dstep 50.0 # torsion step/deg
trnrf 0.95 # trans reduction factor/per cycle quarf 0.95 # quat reduction factor/per cycle dihrf 0.95 # tors reduction factor/per cycle
# Internal Non-Bonded Parameters
intnbp_coeffs 93794.53 83.11 12 6 # C-C internal energy non-bond parameters/Cn intnbp_coeffs 44968.43 57.73 12 6 #C-N_non_bond_parameters/Cn,Cm,n,m
intnbp_coeffs 43400.74 46.71 12 6 # C-O internal energy non-bond parameters/Cn intnbp_coeffs 6530.13 16.72 12 6 # C-H internal energy non-bond parameters/Cn intnbp_coeffs 6530.13 16.72 12 6 # C-X internal energy non-bond parameters/Cn intnbp_coeffs 19667.74 40.3 12 6 #N-N_non_bond_parameters/Cn,Cm,n,m
intnbp_coeffs 18422.13 32.86 12 6 #N-O_non_bond_parameters/Cn,Cm,n,m intnbp_coeffs 2881.2 11.5 12 6 #N-H_non_bond_parameters/Cn,Cm,n,m * intnbp_coeffs 2881.2 11.5 12 6 #N-X_non_bond_parameters/Cn,Cm,n,m *
intnbp_coeffs 16994.07 27.17 12 6 # O-O internal energy non-bond parameters/Cn intnbp_coeffs 4277.26 1349.91 12 10 # O-H internal energy non-bond parameters/Cn intnbp_coeffs 2868.38 9.14 12 6 # O-X internal energy non-bond parameters/Cn intnbp_coeffs 140.66 3.44 12 6 # H-H internal energy non-bond parameters/Cn intnbp_coeffs 140.66 3.44 12 6 # H-X internal energy non-bond parameters/Cn intnbp_coeffs 140.66 3.44 12 6 # X-X internal energy non-bond parameters
#watch sman1.qamb.tors.watch.pdb # real-time monitoring file
outlev 1 # diagnostic output level
# Docked Conformation Clustering Parameters for "analysis" command rmstol 1.0 # cluster tolerance (Angstroms)
rmsref ligandhx.t.pdbqs # reference structure file for RMS calc. #rmsnosym # do no symmetry checking in RMS calc. write_all # write all conformations in a cluster
extnrg 10000. # external grid energy
e0max 0. 10000 # max. allowable initial energy, max. num. retries
# Local Search (Solis & Wets) Parameters (for LS alone and for LGA)
sw_max_its 15000 # number of iterations of Solis & Wets local search sw_max_succ 4 # number of consecutive successes before changing rho
ligandlgasw2.CARB.dpf Page 2 of 2
sw_lb_rho 0.01 # lower bound on rho
ls_search_freq 1.0 # probability of performing local search on an indiv. set_sw1 # set the above pseudo-Solis & Wets parameters
# Genetic Algorithm (GA) and Lamarckian Genetic Algorithm Parameters (LGA) ga_pop_size 50 # number of individuals in population
ga_num_evals 2000000 # maximum number of energy evaluations ga_num_generations 500 # maximum number of generations
ga_elitism 1 # num. of top individuals that automatically survive ga_mutation_rate 0.02 # rate of gene mutation
ga_crossover_rate 0.80 # rate of crossover
ga_window_size 10 # num. of generations for picking worst individual ga_cauchy_alpha 0 # ˜mean of Cauchy distribution for gene mutation ga_cauchy_beta 1 # ˜variance of Cauchy distribution for gene mutation set_ga # set the above parameters for GA or LGA
ga_run 300 # do this many GA or LGA runs
# Perform Cluster Analysis
