def create_rmsd_mmvt_model_input(root_dir):
"""
Create a generic host-guest model input object.
"""
os.chdir(TEST_DIRECTORY)
model_input = common_prepare.Model_input()
model_input.calculation_type = "mmvt"
model_input.calculation_settings = common_prepare.MMVT_input_settings()
model_input.calculation_settings.md_output_interval = 10000
model_input.calculation_settings.md_steps_per_anchor = 100000 #1000000
model_input.temperature = 298.15
model_input.pressure = 1.0
model_input.ensemble = "nvt"
model_input.root_directory = root_dir
model_input.md_program = "openmm"
model_input.constraints = "HBonds"
model_input.rigidWater = True
model_input.hydrogenMass = None
model_input.timestep = 0.002
model_input.nonbonded_cutoff = 0.9
cv_input1 = common_cv.RMSD_cv_input()
cv_input1.group = list(range(147, 162))
pdb_filename = os.path.abspath(
"../data/hostguest_files/hostguest_at0.5.pdb")
cv_input1.ref_structure = pdb_filename
cv_input1.input_anchors = []
rmsd_list = [0.0, 0.5, 1.0]
amber_prmtop_filename = os.path.abspath(
"../data/hostguest_files/hostguest.parm7")
for i, value in enumerate(rmsd_list):
input_anchor = common_cv.RMSD_cv_anchor()
input_anchor.value = value
if i == 0:
assign_amber_params(input_anchor, amber_prmtop_filename,
pdb_filename)
input_anchor.bound_state = False
input_anchor.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor)
model_input.cv_inputs = [cv_input1]
model_input.browndye_settings_input = None
return model_input
metavar="MODEL_INPUT_FILE",
type=str,
help="The name of input XML file for a SEEKR2 calculation.")
argparser.add_argument(
"-f", "--force_overwrite", dest="force_overwrite", default=False,
help="Toggle whether to overwrite existing simulation output files "\
"within any anchor that might have existed in an old model that would "\
"be overwritten by generating this new model. If not toggled, this "\
"program will throw an exception instead of performing any such "\
"overwrite.", action="store_true")
argparser.add_argument(
"-s", "--skip_checks", dest="skip_checks", default=False,
help="By default, pre-simulation checks will be run after the "\
"preparation is complete, and if the checks fail, the SEEKR2 "\
"model will not be saved. This argument bypasses those "\
"checks and allows the model to be generated anyways.",
action="store_true")
args = argparser.parse_args() # parse the args into a dictionary
args = vars(args)
model_input_filename = args["model_input_file"]
force_overwrite = args["force_overwrite"]
skip_checks = args["skip_checks"]
model_input = common_prepare.Model_input()
model_input.deserialize(model_input_filename, user_input=True)
model, xml_path = prepare(model_input, force_overwrite)
if model.anchor_rootdir == ".":
model_dir = os.path.dirname(xml_path)
model.anchor_rootdir = os.path.abspath(model_dir)
if not skip_checks:
check.check_pre_simulation_all(model)
def create_host_guest_mmvt_model_input(root_dir):
"""
Create a generic host-guest model input object.
"""
model_input = common_prepare.Model_input()
model_input.calculation_type = "mmvt"
model_input.calculation_settings = common_prepare.MMVT_input_settings()
model_input.calculation_settings.md_output_interval = 10000
model_input.calculation_settings.md_steps_per_anchor = 1000000
model_input.temperature = 277.8
model_input.pressure = 1.0
model_input.ensemble = "nvt"
model_input.root_directory = root_dir
model_input.md_program = "openmm"
model_input.constraints = "HBonds"
model_input.rigidWater = True
model_input.hydrogenMass = None
model_input.timestep = 0.002
model_input.nonbonded_cutoff = 0.9
cv_input1 = common_cv.Spherical_cv_input()
cv_input1.group1 = list(range(147))
cv_input1.group2 = list(range(147, 162))
cv_input1.input_anchors = []
input_anchor1 = common_cv.Spherical_cv_anchor()
input_anchor1.radius = 0.1
input_anchor1.starting_amber_params = base.Amber_params()
input_anchor1.starting_amber_params.prmtop_filename \
= "../data/hostguest_files/hostguest.parm7"
#input_anchor1.starting_amber_params.inpcrd_filename = \
# "../data/hostguest_files/hostguest.rst7"
input_anchor1.starting_amber_params.pdb_coordinates_filename = \
"../data/hostguest_files/hostguest_at0.4.pdb"
input_anchor1.bound_state = True
input_anchor1.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor1)
input_anchor2 = common_cv.Spherical_cv_anchor()
input_anchor2.radius = 0.2
input_anchor2.starting_amber_params = base.Amber_params()
input_anchor2.starting_amber_params.prmtop_filename = \
"../data/hostguest_files/hostguest.parm7"
#input_anchor2.starting_amber_params.inpcrd_filename = \
# "../data/hostguest_files/hostguest.rst7"
input_anchor2.starting_amber_params.pdb_coordinates_filename = \
"../data/hostguest_files/hostguest_at1.9.pdb"
input_anchor2.bound_state = False
input_anchor2.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor2)
input_anchor3 = common_cv.Spherical_cv_anchor()
input_anchor3.radius = 0.4
input_anchor3.starting_amber_params = base.Amber_params()
input_anchor3.starting_amber_params.prmtop_filename = \
"../data/hostguest_files/hostguest.parm7"
#input_anchor3.starting_amber_params.inpcrd_filename = \
# "../data/hostguest_files/hostguest.rst7"
input_anchor3.starting_amber_params.pdb_coordinates_filename = \
"../data/hostguest_files/hostguest_at3.8.pdb"
input_anchor3.bound_state = False
input_anchor3.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor3)
input_anchor4 = common_cv.Spherical_cv_anchor()
input_anchor4.radius = 0.5
input_anchor4.starting_amber_params = base.Amber_params()
input_anchor4.starting_amber_params.prmtop_filename = \
"../data/hostguest_files/hostguest.parm7"
#input_anchor4.starting_amber_params.inpcrd_filename = \
# "../data/hostguest_files/hostguest.rst7"
input_anchor4.starting_amber_params.pdb_coordinates_filename \
= "../data/hostguest_files/hostguest_at5.4.pdb"
input_anchor4.bound_state = False
input_anchor4.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor4)
input_anchor5 = common_cv.Spherical_cv_anchor()
input_anchor5.radius = 0.7
input_anchor5.starting_amber_params = base.Amber_params()
input_anchor5.starting_amber_params.prmtop_filename \
= "../data/hostguest_files/hostguest.parm7"
#input_anchor5.starting_amber_params.inpcrd_filename \
# = "../data/hostguest_files/hostguest.rst7"
input_anchor5.starting_amber_params.pdb_coordinates_filename \
= "../data/hostguest_files/hostguest_at7.0.pdb"
input_anchor5.bound_state = False
input_anchor5.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor5)
input_anchor6 = common_cv.Spherical_cv_anchor()
input_anchor6.radius = 0.8
input_anchor6.starting_amber_params = base.Amber_params()
input_anchor6.starting_amber_params.prmtop_filename \
= "../data/hostguest_files/hostguest.parm7"
#input_anchor6.starting_amber_params.inpcrd_filename \
# = "../data/hostguest_files/hostguest.rst7"
input_anchor6.starting_amber_params.pdb_coordinates_filename \
= "../data/hostguest_files/hostguest_at8.3.pdb"
input_anchor6.bound_state = False
input_anchor6.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor6)
input_anchor7 = common_cv.Spherical_cv_anchor()
input_anchor7.radius = 1.0
input_anchor7.starting_amber_params = base.Amber_params()
input_anchor7.starting_amber_params.prmtop_filename \
= "../data/hostguest_files/hostguest.parm7"
#input_anchor7.starting_amber_params.inpcrd_filename \
# = "../data/hostguest_files/hostguest.rst7"
input_anchor7.starting_amber_params.pdb_coordinates_filename \
= "../data/hostguest_files/hostguest_at9.8.pdb"
input_anchor7.bound_state = False
input_anchor7.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor7)
input_anchor8 = common_cv.Spherical_cv_anchor()
input_anchor8.radius = 1.1
input_anchor8.starting_amber_params = base.Amber_params()
input_anchor8.starting_amber_params.prmtop_filename \
= "../data/hostguest_files/hostguest.parm7"
#input_anchor8.starting_amber_params.inpcrd_filename \
# = "../data/hostguest_files/hostguest.rst7"
input_anchor8.starting_amber_params.pdb_coordinates_filename \
= "../data/hostguest_files/hostguest_at11.2.pdb"
input_anchor8.bound_state = False
input_anchor8.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor8)
input_anchor9 = common_cv.Spherical_cv_anchor()
input_anchor9.radius = 1.3
input_anchor9.starting_amber_params = base.Amber_params()
input_anchor9.starting_amber_params.prmtop_filename \
= "../data/hostguest_files/hostguest.parm7"
#input_anchor9.starting_amber_params.inpcrd_filename \
# = "../data/hostguest_files/hostguest.rst7"
input_anchor9.starting_amber_params.pdb_coordinates_filename \
= "../data/hostguest_files/hostguest_at12.8.pdb"
input_anchor9.bound_state = False
input_anchor9.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor9)
input_anchor10 = common_cv.Spherical_cv_anchor()
input_anchor10.radius = 1.4
input_anchor10.starting_amber_params = base.Amber_params()
input_anchor10.starting_amber_params.prmtop_filename \
= "../data/hostguest_files/hostguest.parm7"
#input_anchor10.starting_amber_params.inpcrd_filename \
# = "../data/hostguest_files/hostguest.rst7"
input_anchor10.starting_amber_params.pdb_coordinates_filename \
= "../data/hostguest_files/hostguest_at9.5.pdb"
input_anchor10.bound_state = False
input_anchor10.bulk_anchor = True
cv_input1.input_anchors.append(input_anchor10)
input_anchor11 = common_cv.Spherical_cv_anchor()
input_anchor11.radius = 1.05
input_anchor11.starting_amber_params = base.Amber_params()
input_anchor11.starting_amber_params.prmtop_filename \
= "../data/hostguest_files/hostguest.parm7"
#input_anchor11.starting_amber_params.inpcrd_filename \
# = "../data/hostguest_files/hostguest.rst7"
input_anchor11.starting_amber_params.pdb_coordinates_filename \
= "../data/hostguest_files/hostguest_at10.5.pdb"
input_anchor11.bound_state = False
input_anchor11.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor11)
input_anchor12 = common_cv.Spherical_cv_anchor()
input_anchor12.radius = 1.15
input_anchor12.starting_amber_params = base.Amber_params()
input_anchor12.starting_amber_params.prmtop_filename \
= "../data/hostguest_files/hostguest.parm7"
#input_anchor12.starting_amber_params.inpcrd_filename \
# = "../data/hostguest_files/hostguest.rst7"
input_anchor12.starting_amber_params.pdb_coordinates_filename \
= "../data/hostguest_files/hostguest_at11.5.pdb"
input_anchor12.bound_state = False
input_anchor12.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor12)
input_anchor13 = common_cv.Spherical_cv_anchor()
input_anchor13.radius = 1.25
input_anchor13.starting_amber_params = base.Amber_params()
input_anchor13.starting_amber_params.prmtop_filename \
= "../data/hostguest_files/hostguest.parm7"
#input_anchor13.starting_amber_params.inpcrd_filename \
# = "../data/hostguest_files/hostguest.rst7"
input_anchor13.starting_amber_params.pdb_coordinates_filename \
= "../data/hostguest_files/hostguest_at12.5.pdb"
input_anchor13.bound_state = False
input_anchor13.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor13)
input_anchor14 = common_cv.Spherical_cv_anchor()
input_anchor14.radius = 1.35
input_anchor14.starting_amber_params = base.Amber_params()
input_anchor14.starting_amber_params.prmtop_filename \
= ""
#input_anchor14.starting_amber_params.inpcrd_filename \
# = ""
input_anchor14.starting_amber_params.pdb_coordinates_filename \
= ""
input_anchor14.bound_state = False
input_anchor14.bulk_anchor = True
cv_input1.input_anchors.append(input_anchor14)
model_input.cv_inputs = [cv_input1]
model_input.browndye_settings_input \
= common_prepare.Browndye_settings_input()
model_input.browndye_settings_input.binary_directory = ""
model_input.browndye_settings_input.receptor_pqr_filename \
= "../data/hostguest_files/hostguest_receptor.pqr"
model_input.browndye_settings_input.ligand_pqr_filename \
= "../data/hostguest_files/hostguest_ligand.pqr"
model_input.browndye_settings_input.apbs_grid_spacing = 0.5
model_input.browndye_settings_input.receptor_indices = list(range(147))
model_input.browndye_settings_input.ligand_indices = list(range(15))
ion1 = base.Ion()
ion1.radius = 1.2
ion1.charge = -1.0
ion1.conc = 0.0
ion2 = base.Ion()
ion2.radius = 0.9
ion2.charge = 1.0
ion2.conc = 0.0
model_input.browndye_settings_input.ions = [ion1, ion2]
model_input.browndye_settings_input.num_bd_milestone_trajectories = 1000
model_input.browndye_settings_input.num_b_surface_trajectories = 10000
model_input.browndye_settings_input.max_b_surface_trajs_to_extract = 1000
model_input.browndye_settings_input.n_threads = 1
return model_input
def create_toy_multi_model_input(root_dir):
"""
Create a toy mmvt multidimensional model input.
This is the Entropy barrier system.
"""
os.chdir(TEST_DIRECTORY)
model_input = common_prepare.Model_input()
model_input.calculation_type = "mmvt"
model_input.calculation_settings = common_prepare.MMVT_input_settings()
model_input.calculation_settings.md_output_interval = 1000
model_input.calculation_settings.md_steps_per_anchor = 100000
model_input.temperature = 300.0
model_input.pressure = 1.0
model_input.ensemble = "nvt"
model_input.root_directory = root_dir
model_input.md_program = "openmm"
model_input.constraints = "none"
model_input.rigidWater = True
model_input.hydrogenMass = None
model_input.integrator_type = "langevin"
model_input.timestep = 0.002
model_input.nonbonded_cutoff = None
combo = common_cv.Grid_combo()
cv_input1 = common_cv.Toy_cv_input()
cv_input1.groups = [[0]]
cv_input1.variable_name = "value"
cv_input1.cv_expression = "x1"
cv_input1.openmm_expression = "step(k*(x1-value))"
cv_input1.input_anchors = []
cv_input2 = common_cv.Toy_cv_input()
cv_input2.groups = [[0]]
cv_input2.variable_name = "value"
cv_input2.cv_expression = "y1"
cv_input2.openmm_expression = "step(k*(y1-value))"
cv_input2.input_anchors = []
values_list = [-0.7, -0.5, -0.3, -0.1, 0.1, 0.3, 0.5, 0.7]
for i, value in enumerate(values_list):
input_anchor = common_cv.Toy_cv_anchor()
input_anchor.value = value
input_anchor.starting_positions = None
input_anchor.bound_state = False
input_anchor.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor)
for i, value in enumerate(values_list):
input_anchor = common_cv.Toy_cv_anchor()
input_anchor.value = value
input_anchor.starting_positions = None
input_anchor.bound_state = False
input_anchor.bulk_anchor = False
cv_input2.input_anchors.append(input_anchor)
combo.cv_inputs = [cv_input1, cv_input2]
stateA = common_cv.State_point()
stateA.name = "stateA"
stateA.location = [0.1, -0.7, 0.0]
stateB = common_cv.State_point()
stateB.name = "stateB"
stateB.location = [0.1, 0.7, 0.0]
combo.state_points = [stateA, stateB]
model_input.cv_inputs = [combo]
model_input.browndye_settings_input = None
model_input.toy_settings_input = common_prepare.Toy_settings_input()
model_input.toy_settings_input.potential_energy_expression \
= "5*(x1^6+y1^6+exp(-(10*y1)^2)*(1-exp(-(10*x1)^2)))"
model_input.toy_settings_input.num_particles = 1
model_input.toy_settings_input.masses = np.array([10.0])
return model_input
def create_toy_mmvt_model_input(root_dir):
"""
Create a toy mmvt model input.
This is the Entropy barrier system.
"""
os.chdir(TEST_DIRECTORY)
model_input = common_prepare.Model_input()
model_input.calculation_type = "mmvt"
model_input.calculation_settings = common_prepare.MMVT_input_settings()
model_input.calculation_settings.md_output_interval = 1000
model_input.calculation_settings.md_steps_per_anchor = 100000
model_input.temperature = 300.0
model_input.pressure = 1.0
model_input.ensemble = "nvt"
model_input.root_directory = root_dir
model_input.md_program = "openmm"
model_input.constraints = "none"
model_input.rigidWater = True
model_input.hydrogenMass = None
model_input.integrator_type = "langevin"
model_input.timestep = 0.002
model_input.nonbonded_cutoff = None
cv_input1 = common_cv.Toy_cv_input()
cv_input1.groups = [[0]]
cv_input1.variable_name = "value"
cv_input1.cv_expression = "y1"
#cv_input1.openmm_expression = "step(k*(y1-value))"
cv_input1.input_anchors = []
values_list = [-0.7, -0.5, -0.3, -0.1, 0.1, 0.3, 0.5, 0.7]
positions_list = [
[[[0.0, -0.7, 0.0]], [[0.3, -0.7, 0.0]]],
[[[0.0, -0.5, 0.0]]],
[[[0.0, -0.3, 0.0]]],
[[[0.0, -0.1, 0.0]]],
[[[0.0, 0.1, 0.0]]],
[[[0.0, 0.3, 0.0]]],
[[[0.0, 0.5, 0.0]]],
[[[0.0, 0.7, 0.0]]]]
for i, (value, position) in enumerate(zip(values_list, positions_list)):
input_anchor = common_cv.Toy_cv_anchor()
input_anchor.value = value
input_anchor.starting_positions = np.array(position)
if i == 0:
input_anchor.bound_state = True
else:
input_anchor.bound_state = False
if i == len(values_list)-1:
input_anchor.bulk_anchor = True
else:
input_anchor.bulk_anchor = False
#input_anchor.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor)
model_input.cv_inputs = [cv_input1]
model_input.browndye_settings_input = None
model_input.toy_settings_input = common_prepare.Toy_settings_input()
model_input.toy_settings_input.potential_energy_expression \
= "5*(x1^6+y1^6+exp(-(10*y1)^2)*(1-exp(-(10*x1)^2)))"
model_input.toy_settings_input.num_particles = 1
model_input.toy_settings_input.masses = np.array([10.0])
return model_input
def create_host_guest_mmvt_model_input(root_dir, bd=True, ff="amber"):
"""
Create a generic host-guest model input object.
"""
os.chdir(TEST_DIRECTORY)
model_input = common_prepare.Model_input()
model_input.calculation_type = "mmvt"
model_input.calculation_settings = common_prepare.MMVT_input_settings()
model_input.calculation_settings.md_output_interval = 10000
model_input.calculation_settings.md_steps_per_anchor = 100000 #1000000
model_input.temperature = 298.15
model_input.pressure = 1.0
model_input.ensemble = "nvt"
model_input.root_directory = root_dir
model_input.md_program = "openmm"
model_input.constraints = "HBonds"
model_input.rigidWater = True
model_input.hydrogenMass = None
model_input.timestep = 0.002
model_input.nonbonded_cutoff = 0.9
cv_input1 = common_cv.Spherical_cv_input()
cv_input1.group1 = list(range(147))
cv_input1.group2 = list(range(147, 162))
cv_input1.input_anchors = []
radius_list = [0.05, 0.15, 0.25, 0.35, 0.45, 0.55, 0.65, 0.75, 0.85, 0.95,
1.05, 1.15, 1.25, 1.35]
amber_prmtop_filename = os.path.abspath(
"../data/hostguest_files/hostguest.parm7")
forcefield_built_in_ff_list = ["amber14/tip3pfb.xml"]
forcefield_custom_ff_list = [os.path.abspath(
"../data/hostguest_files/hostguest.xml")]
pdb_filenames = [os.path.abspath(
"../data/hostguest_files/hostguest_at0.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at1.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at2.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at3.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at4.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at5.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at6.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at7.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at8.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at9.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at10.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at11.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at12.5.pdb"),
""]
for i, (radius, pdb_filename) in enumerate(zip(radius_list, pdb_filenames)):
input_anchor = common_cv.Spherical_cv_anchor()
input_anchor.radius = radius
if ff == "amber":
assign_amber_params(input_anchor, amber_prmtop_filename,
pdb_filename)
elif ff == "forcefield":
print("test pdb_filename:", pdb_filename)
assign_forcefield_params(input_anchor, forcefield_built_in_ff_list,
forcefield_custom_ff_list, pdb_filename)
else:
raise Exception("ff type not supported: {}".format(ff))
if i == 0:
input_anchor.bound_state = True
else:
input_anchor.bound_state = False
if i == len(radius_list)-1:
input_anchor.bulk_anchor = True
else:
input_anchor.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor)
model_input.cv_inputs = [cv_input1]
if bd:
model_input.browndye_settings_input \
= common_prepare.Browndye_settings_input()
model_input.browndye_settings_input.binary_directory = ""
model_input.browndye_settings_input.receptor_pqr_filename \
= os.path.abspath("../data/hostguest_files/hostguest_receptor.pqr")
model_input.browndye_settings_input.ligand_pqr_filename \
= os.path.abspath("../data/hostguest_files/hostguest_ligand.pqr")
model_input.browndye_settings_input.apbs_grid_spacing = 0.5
model_input.browndye_settings_input.receptor_indices = list(range(147))
model_input.browndye_settings_input.ligand_indices = list(range(15))
ion1 = base.Ion()
ion1.radius = 1.2
ion1.charge = -1.0
ion1.conc = 0.0
ion2 = base.Ion()
ion2.radius = 0.9
ion2.charge = 1.0
ion2.conc = 0.0
model_input.browndye_settings_input.ions = [ion1, ion2]
#model_input.browndye_settings_input.num_bd_milestone_trajectories = 100
model_input.browndye_settings_input.num_b_surface_trajectories = 100
#model_input.browndye_settings_input.max_b_surface_trajs_to_extract = 100
model_input.browndye_settings_input.n_threads = 1
else:
model_input.browndye_settings_input = None
return model_input
def create_tiwary_mmvt_model_input(root_dir):
"""
Create a generic host-guest model input object.
"""
os.chdir(TEST_DIRECTORY)
model_input = common_prepare.Model_input()
model_input.calculation_type = "mmvt"
model_input.calculation_settings = common_prepare.MMVT_input_settings()
model_input.calculation_settings.md_output_interval = 10000
model_input.calculation_settings.md_steps_per_anchor = 100000 #1000000
model_input.temperature = 298.15
model_input.pressure = 1.0
model_input.ensemble = "nvt"
model_input.root_directory = root_dir
model_input.md_program = "openmm"
model_input.constraints = "HBonds"
model_input.rigidWater = True
model_input.hydrogenMass = None
model_input.timestep = 0.002
model_input.nonbonded_cutoff = 0.9
order_parameter1 = common_cv.Tiwary_cv_distance_order_parameter()
order_parameter1.group1 = [
0, 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, 52, 53, 54, 55, 56, 57, 58,
59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72,
73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,
101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,
112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122,
123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133,
134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144,
145, 146]
order_parameter1.group2 = [
147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157,
158, 159, 160, 161]
order_parameter2 = common_cv.Tiwary_cv_angle_order_parameter()
order_parameter2.group1 = [0]
order_parameter2.group2 = [147]
order_parameter2.group3 = [161]
order_parameter3 = common_cv.Tiwary_cv_angle_order_parameter()
order_parameter3.group1 = [0]
order_parameter3.group2 = [1]
order_parameter3.group3 = [147]
order_parameter3.group4 = [161]
order_parameters = [order_parameter1, order_parameter2, order_parameter3]
order_parameter_weights1 = [0.99, 0.005, 0.005]
order_parameter_weights2 = [0.97, 0.015, 0.015]
cv_input1 = common_cv.Tiwary_cv_input()
cv_input1.order_parameters = order_parameters
cv_input1.order_parameter_weights = order_parameter_weights1
cv_input1.input_anchors = []
cv_input2 = common_cv.Tiwary_cv_input()
cv_input2.order_parameters = order_parameters
cv_input2.order_parameter_weights = order_parameter_weights2
cv_input2.input_anchors = []
cv_input3 = common_cv.Spherical_cv_input()
cv_input3.group1 = list(range(147))
cv_input3.group2 = list(range(147, 162))
cv_input3.input_anchors = []
values_list1 = [0.05, 0.15, 0.25, 0.35, 0.45, 0.55]
values_list2 = [0.55, 0.65, 0.75, 0.85, 0.95, 1.05, 1.15]
spherical_radii = [1.15, 1.25, 1.35]
amber_prmtop_filename = os.path.abspath(
"../data/hostguest_files/hostguest.parm7")
pdb_filenames1 = [os.path.abspath(
"../data/hostguest_files/hostguest_at0.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at1.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at2.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at3.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at4.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at5.5.pdb"),]
pdb_filenames2 = ["",
os.path.abspath(
"../data/hostguest_files/hostguest_at6.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at7.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at8.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at9.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at10.5.pdb"),
os.path.abspath(
"../data/hostguest_files/hostguest_at11.5.pdb"),]
pdb_filenames3 = ["",
os.path.abspath(
"../data/hostguest_files/hostguest_at12.5.pdb"),
""]
for i, (value, pdb_filename) in enumerate(zip(values_list1, pdb_filenames1)):
input_anchor = common_cv.Tiwary_cv_anchor()
input_anchor.value = value
assign_amber_params(input_anchor, amber_prmtop_filename,
pdb_filename)
if i == 0:
input_anchor.bound_state = True
else:
input_anchor.bound_state = False
input_anchor.bulk_anchor = False
cv_input1.input_anchors.append(input_anchor)
cv_input1.input_anchors[-1].connection_flags = [1]
for i, (value, pdb_filename) in enumerate(zip(values_list2, pdb_filenames2)):
input_anchor = common_cv.Tiwary_cv_anchor()
input_anchor.value = value
assign_amber_params(input_anchor, amber_prmtop_filename,
pdb_filename)
input_anchor.bound_state = False
input_anchor.bulk_anchor = False
cv_input2.input_anchors.append(input_anchor)
cv_input2.input_anchors[0].connection_flags = [1]
cv_input2.input_anchors[-1].connection_flags = [2]
for i, (radius, pdb_filename) in enumerate(zip(spherical_radii, pdb_filenames3)):
input_anchor = common_cv.Spherical_cv_anchor()
input_anchor.radius = radius
assign_amber_params(input_anchor, amber_prmtop_filename,
pdb_filename)
input_anchor.bound_state = False
if i == len(pdb_filenames3)-1:
input_anchor.bulk_anchor = True
else:
input_anchor.bulk_anchor = False
cv_input3.input_anchors.append(input_anchor)
cv_input3.input_anchors[0].connection_flags = [2]
model_input.cv_inputs = [cv_input1, cv_input2, cv_input3]
return model_input