ligandmin.dpf Page 1 of 2
seed time pid # for random number generator types CNOHX # atom type names
fld proteinhx.AD1.fld # grid data file
map proteinhx.AD1.C.map # C-atomic affinity map file map proteinhx.AD1.N.map # N-atomic affinity map file map proteinhx.AD1.O.map # O-atomic affinity map file map proteinhx.AD1.H.map # H-atomic affinity map file map proteinhx.AD1.X.map # X-atomic affinity map file map proteinhx.AD1.e.map # electrostatics map file
move ligandhx.t.pdbqs # small molecule file
about 3.544 65.710 64.546 # small molecule center
# Initial Translation, Quaternion and Torsions
tran0 3.544 65.710 64.546 # initial coordinates/A or "random" quat0 1. 0. 0. 0. # initial quaternion or "random" ndihe 4 # number of initial torsions
dihe0 0. 0. 0. 0. # initial torsions
torsdof 1 0.3113 # num. non-Hydrogen torsional DOF & coeff.
# Initial Translation, Quaternion and Torsion Step Sizes and Reduction Factors tstep 0.1 # translation step/A
qstep 1.0 # quaternion step/deg dstep 1.0 # 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 1272653.000 1127.684 12 6 # C-C internal energy non-bond parameters/Cn intnbp_coeffs 610155.100 783.345 12 6 #C-N_non_bond_parameters/Cn,Cm,n,m
intnbp_coeffs 588883.800 633.754 12 6 # C-O internal energy non-bond parameters/Cn intnbp_coeffs 88604.240 226.910 12 6 # C-H internal energy non-bond parameters/Cn intnbp_coeffs 88604.240 226.910 12 6 # C-X internal energy non-bond parameters/Cn intnbp_coeffs 266862.2 546.7653 12 6 #N-N_non_bond_parameters/Cn,Cm,n,m
intnbp_coeffs 249961.0 445.9175 12 6 #N-O_non_bond_parameters/Cn,Cm,n,m intnbp_coeffs 75570.000 23850.000 12 10 #N-H_non_bond_parameters/Cn,Cm,n,m * intnbp_coeffs 39093.66 155.9833 12 6 #N-X_non_bond_parameters/Cn,Cm,n,m *
intnbp_coeffs 230584.400 368.677 12 6 # O-O internal energy non-bond parameters/Cn intnbp_coeffs 75570.000 23850.000 12 10 # O-H internal energy non-bond parameters/Cn intnbp_coeffs 38919.640 124.049 12 6 # O-X internal energy non-bond parameters/Cn intnbp_coeffs 1908.578 46.738 12 6 # H-H internal energy non-bond parameters/Cn intnbp_coeffs 1908.578 46.738 12 6 # H-X internal energy non-bond parameters/Cn intnbp_coeffs 1908.578 46.738 12 6 # X-X internal energy non-bond parameters
#intelec # calculate internal electrostatic energy
#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 qligandhx.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 1000. # external grid energy
e0max 0. 4 # max. allowable initial energy, max. num. retries
ligandmin.dpf Page 2 of 2
sw_max_fail 4 # number of 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 1.0 # probability of performing local search on an indiv. set_sw1 # set the above pseudo-Solis & Wets parameters
do_local 100
