using 12/12 available cores
using random number seed of -1
*** Directories ***
start: /Users/dminh/Documents/Code/AlGDock-0.0.1/Example
BC: /Users/dminh/Documents/Code/AlGDock-0.0.1/Example/BC
CD: /Users/dminh/Documents/Code/AlGDock-0.0.1/Example/CD
*** Files ***
previously stored in BC directory:
prmtop:
L: prmtopcrd/ligand.prmtop
ligand_database: prmtopcrd/ligand.db
forcefield: prmtopcrd/gaff2.dat
inpcrd:
L: prmtopcrd/ligand.trans.inpcrd
previously stored in CD directory:
namd: ../../../../../../Applications/NAMD_2.13_MacOSX-x86_64-multicore/namd2
receptor_database: prmtopcrd/receptor.db
prmtop:
L: prmtopcrd/ligand.prmtop
R: prmtopcrd/receptor.prmtop
RL: prmtopcrd/complex.prmtop
ligand_database: prmtopcrd/ligand.db
dir_BC: BC
fixed_atoms:
R: prmtopcrd/receptor.pdb
RL: prmtopcrd/complex.pdb
grids:
LJr: grids/LJr.nc
LJa: grids/LJa.nc
sELE: grids/pbsa.nc
ELE: grids/direct_ELE.nc
desolv: grids/desolv.nc
mol2:
L: prmtopcrd/ligand.mol2
score: prmtopcrd/xtal_plus_dock6_scored.mol2
forcefield: prmtopcrd/gaff2.dat
inpcrd:
L: prmtopcrd/ligand.trans.inpcrd
R: prmtopcrd/receptor.trans.inpcrd
RL: prmtopcrd/complex.trans.inpcrd
from arguments and defaults:
ligand_database: prmtopcrd/ligand.db
receptor_database: prmtopcrd/receptor.db
forcefield: prmtopcrd/gaff2.dat
prmtop:
L: prmtopcrd/ligand.prmtop
R: prmtopcrd/receptor.prmtop
RL: prmtopcrd/complex.prmtop
inpcrd:
L: prmtopcrd/ligand.trans.inpcrd
R: prmtopcrd/receptor.trans.inpcrd
RL: prmtopcrd/complex.trans.inpcrd
mol2:
L: prmtopcrd/ligand.mol2
fixed_atoms:
R: prmtopcrd/receptor.pdb
RL: prmtopcrd/complex.pdb
grids:
LJr: grids/LJr.nc
LJa: grids/LJa.nc
sELE: grids/pbsa.nc
ELE: grids/direct_ELE.nc
desolv: grids/desolv.nc
score: prmtopcrd/xtal_plus_dock6_scored.mol2
dir_BC: BC
to be used:
ligand_database: prmtopcrd/ligand.db
receptor_database: prmtopcrd/receptor.db
forcefield: prmtopcrd/gaff2.dat
frcmodList: ['/Users/dminh/Documents/Code/AlGDock-0.0.1/Example/prmtopcrd/ligand.frcmod']
prmtop:
L: prmtopcrd/ligand.prmtop
R: prmtopcrd/receptor.prmtop
RL: prmtopcrd/complex.prmtop
inpcrd:
L: prmtopcrd/ligand.trans.inpcrd
R: prmtopcrd/receptor.trans.inpcrd
RL: prmtopcrd/complex.trans.inpcrd
mol2:
L: prmtopcrd/ligand.mol2
fixed_atoms:
R: prmtopcrd/receptor.pdb
RL: prmtopcrd/complex.pdb
grids:
LJr: grids/LJr.nc
LJa: grids/LJa.nc
sELE: grids/pbsa.nc
ELE: grids/direct_ELE.nc
desolv: grids/desolv.nc
score: prmtopcrd/xtal_plus_dock6_scored.mol2
dir_BC: BC
namd: ../../../../../../Applications/NAMD_2.13_MacOSX-x86_64-multicore/namd2
*** Simulation parameters and constants ***
for BC:
protocol: Adaptive
therm_speed: 25.0
T_HIGH: 450.0
T_SIMMIN: 300.0
T_TARGET: 300.0
H_mass: 4.0
delta_t: 4.0
sampler: HMC
steps_per_seed: 200
seeds_per_state: 10
darts_per_seed: 0
repX_cycles: 3
min_repX_acc: 0.4
sweeps_per_cycle: 50
snaps_per_cycle: 25
attempts_per_sweep: 100
steps_per_sweep: 50
darts_per_sweep: 0
phases: ['NAMD_Gas', 'OpenMM_OBC2']
sampling_importance_resampling: True
solvation: Full
keep_intermediate: True
GMC_attempts: 0
GMC_tors_threshold: 0.0
for CD:
protocol: Adaptive
therm_speed: 0.25
T_HIGH: 450.0
T_SIMMIN: 300.0
T_TARGET: 300.0
H_mass: 4.0
delta_t: 4.0
sampler: HMC
steps_per_seed: 200
seeds_per_state: 10
darts_per_seed: 0
repX_cycles: 4
min_repX_acc: 0.4
sweeps_per_cycle: 50
snaps_per_cycle: 25
attempts_per_sweep: 100
steps_per_sweep: 50
darts_per_sweep: 0
phases: ['NAMD_Gas', 'OpenMM_OBC2']
sampling_importance_resampling: True
solvation: Full
keep_intermediate: True
GMC_attempts: 0
GMC_tors_threshold: 0.0
temperature_scaling: Quadratic
site: Sphere
site_center: array([ 1.7416, 1.7416, 1.7416])
site_max_R: 1.0
site_density: 10.0
pose: -1
k_pose: 1000.0
MCMC_moves: 1
rmsd: True
receptor_NAMD_Gas: array([[ 0., 0., 0., 0., 0., 0., 0., 0.]])
ligand residue name: iga
*** Simulation parameters and constants ***
for BC:
protocol: Adaptive
therm_speed: 25.0
T_HIGH: 450.0
T_SIMMIN: 300.0
T_TARGET: 300.0
H_mass: 4.0
delta_t: 4.0
sampler: HMC
steps_per_seed: 200
seeds_per_state: 10
darts_per_seed: 0
repX_cycles: 3
min_repX_acc: 0.4
sweeps_per_cycle: 50
snaps_per_cycle: 25
attempts_per_sweep: 100
steps_per_sweep: 50
darts_per_sweep: 0
phases: ['NAMD_Gas', 'OpenMM_OBC2']
sampling_importance_resampling: True
solvation: Full
keep_intermediate: True
GMC_attempts: 0
GMC_tors_threshold: 0.0
for CD:
protocol: Adaptive
therm_speed: 0.25
T_HIGH: 450.0
T_SIMMIN: 300.0
T_TARGET: 300.0
H_mass: 4.0
delta_t: 4.0
sampler: HMC
steps_per_seed: 200
seeds_per_state: 10
darts_per_seed: 0
repX_cycles: 4
min_repX_acc: 0.4
sweeps_per_cycle: 50
snaps_per_cycle: 25
attempts_per_sweep: 100
steps_per_sweep: 50
darts_per_sweep: 0
phases: ['NAMD_Gas', 'OpenMM_OBC2']
sampling_importance_resampling: True
solvation: Full
keep_intermediate: True
GMC_attempts: 0
GMC_tors_threshold: 0.0
temperature_scaling: Quadratic
site: Sphere
site_center: array([ 1.7416, 1.7416, 1.7416])
site_max_R: 1.0
site_density: 10.0
pose: -1
k_pose: 1000.0
MCMC_moves: 1
rmsd: True
receptor_NAMD_Gas: array([[ 0., 0., 0., 0., 0., 0., 0., 0.]])