def test_write_xml_parameters_methanol_ions_energy(self):
""" Test writing XML parameter files from Charmm parameter files, reading them back into OpenMM ForceField, and computing energy of methanol and NaCl """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(get_fn('par_all36_cgenff.prm'),
get_fn('top_all36_cgenff.rtf'),
get_fn('toppar_water_ions.str')) # WARNING: contains duplicate water templates
)
del params.residues['TP3M'] # Delete to avoid duplicate water template topologies
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(
OriginalFile='par_all36_cgenff.prm, top_all36_cgenff.rtf, toppar_water_ions.str',
Reference='MacKerrell'
)
)
forcefield = app.ForceField(ffxml_filename)
# Parameterize methanol and ions in vacuum
pdbfile = app.PDBFile(get_fn('methanol_ions.pdb'))
system = forcefield.createSystem(pdbfile.topology, nonbondedMethod=app.NoCutoff)
integrator = mm.VerletIntegrator(1.0*u.femtoseconds)
context = mm.Context(system, integrator, CPU)
context.setPositions(pdbfile.positions)
ffxml_potential = context.getState(getEnergy=True).getPotentialEnergy() / u.kilocalories_per_mole
del context, integrator
# Compute energy via ParmEd reader
psf = CharmmPsfFile(get_fn('methanol_ions.psf'))
system = psf.createSystem(params)
integrator = mm.VerletIntegrator(1.0*u.femtoseconds)
context = mm.Context(system, integrator, CPU)
context.setPositions(pdbfile.positions)
parmed_potential = context.getState(getEnergy=True).getPotentialEnergy() / u.kilocalories_per_mole
del context, integrator
# Ensure potentials are almost equal
self.assertAlmostEqual(ffxml_potential, parmed_potential)
def test_write_xml_parameters_methanol_ions_energy(self):
""" Test writing XML parameter files from Charmm parameter files, reading them back into OpenMM ForceField, and computing energy of methanol and NaCl """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(get_fn('par_all36_cgenff.prm'),
get_fn('top_all36_cgenff.rtf'),
get_fn('toppar_water_ions.str')) # WARNING: contains duplicate water templates
)
del params.residues['TP3M'] # Delete to avoid duplicate water template topologies
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(
OriginalFile='par_all36_cgenff.prm, top_all36_cgenff.rtf, toppar_water_ions.str',
Reference='MacKerrell'
)
)
forcefield = app.ForceField(ffxml_filename)
# Parameterize methanol and ions in vacuum
pdbfile = app.PDBFile(get_fn('methanol_ions.pdb'))
system = forcefield.createSystem(pdbfile.topology, nonbondedMethod=app.NoCutoff)
integrator = mm.VerletIntegrator(1.0*u.femtoseconds)
context = mm.Context(system, integrator, CPU)
context.setPositions(pdbfile.positions)
ffxml_potential = context.getState(getEnergy=True).getPotentialEnergy() / u.kilocalories_per_mole
del context, integrator
# Compute energy via ParmEd reader
psf = CharmmPsfFile(get_fn('methanol_ions.psf'))
system = psf.createSystem(params)
integrator = mm.VerletIntegrator(1.0*u.femtoseconds)
context = mm.Context(system, integrator, CPU)
context.setPositions(pdbfile.positions)
parmed_potential = context.getState(getEnergy=True).getPotentialEnergy() / u.kilocalories_per_mole
del context, integrator
# Ensure potentials are almost equal
self.assertAlmostEqual(ffxml_potential, parmed_potential)
def test_add_charmm_psf(self):
""" Test adding CHARMM PSF file to ParmList """
parms = ParmList()
ala3 = CharmmPsfFile(get_fn('ala3_solv.psf'))
aaa = CharmmPsfFile(get_fn('ala_ala_ala.psf'))
xaaa = CharmmPsfFile(get_fn('ala_ala_ala.psf.xplor'))
aaaa = CharmmPsfFile(get_fn('ala_ala_ala_autopsf.psf'))
parms.add_parm(ala3)
parms.add_parm(aaa)
parms.add_parm(xaaa)
parms.add_parm(aaaa)
# Check indexing
self.assertIs(parms[0], ala3)
self.assertIs(parms[1], aaa)
self.assertIs(parms[2], xaaa)
self.assertIs(parms[3], aaaa)
# Test name indexing
self.assertIs(parms[get_fn('ala3_solv.psf')], ala3)
self.assertIs(parms[get_fn('ala_ala_ala.psf')], aaa)
self.assertIs(parms[get_fn('ala_ala_ala.psf.xplor')], xaaa)
self.assertIs(parms[get_fn('ala_ala_ala_autopsf.psf')], aaaa)
# Check that the last parm added is active
self.assertIs(parms.parm, parms[-1])
# Set a new active topology
parms.set_new_active(0)
self.assertIs(parms.parm, ala3)
parms.set_new_active(get_fn('ala_ala_ala.psf'))
self.assertIs(parms.parm, aaa)
def __init__(self, true_value=None, initial_value=None, n_increments=18, rj=True, sample_phase=False,
continuous=False):
self._param = CharmmParameterSet(get_fun('toy.str'))
self._struct = CharmmPsfFile(get_fun('toy.psf'))
self._pdb = app.PDBFile(get_fun('toy.pdb'))
self._topology = md.load_psf(get_fun('toy.psf'))
self.synthetic_energy = units.Quantity()
self._positions = units.Quantity()
self._platform = mm.Platform.getPlatformByName('Reference')
# Replace ('CG331', 'CG321', 'CG321', 'CG331') torsion with true_value
self._dih_type = ('CG331', 'CG321', 'CG321', 'CG331')
original_torsion = self._param.dihedral_types[self._dih_type]
if true_value is not None:
if type(true_value) == DihedralTypeList:
dih_tlist = true_value
elif type(true_value) == DihedralType:
dih_tlist = DihedralTypeList()
dih_tlist.append(true_value)
else:
dih_tlist = self._randomize_dih_param(return_dih=True)
self.true_value = copy.deepcopy(dih_tlist)
self._param.dihedral_types[self._dih_type] = dih_tlist
# parametrize toy
self._struct.load_parameters(self._param, copy_parameters=False)
self._struct.positions = self._pdb.positions
# generate synthetic torsion scan
self._torsion_scan(n_increments=n_increments)
# initialize parameter
if initial_value is not None:
if type(initial_value) == DihedralTypeList:
dih_tlist = initial_value
if type(initial_value) == DihedralType:
dih_tlist = DihedralTypeList()
dih_tlist.append(initial_value)
elif initial_value == 'cgenff':
dih_tlist = original_torsion
else:
dih_tlist = self._randomize_dih_param(return_dih=True)
self.initial_value = copy.deepcopy(dih_tlist)
self._param.dihedral_types[self._dih_type] = dih_tlist
# create torsionfit.TorsionScanSet
torsions = np.zeros((len(self._positions), 4))
torsions[:] = [1, 2, 3, 4]
direction = None
steps = None
self.scan_set = ScanSet.QMDataBase(positions=self._positions.value_in_unit(units.nanometers),
topology=self._topology, structure=self._struct, torsions=torsions,
steps=steps, directions=direction,
qm_energies=self.synthetic_energy.value_in_unit(units.kilojoules_per_mole))
self.model = model.TorsionFitModel(param=self._param, frags=self.scan_set, platform=self._platform,
param_to_opt=[self._dih_type], rj=rj, continuous_phase=continuous,
sample_phase=sample_phase)
def test_create_simple_system(self):
psf = CharmmPsfFile(get_fn("ala3_solv_drude.psf"))
crd = CharmmCrdFile(get_fn("ala3_solv_drude.crd"))
params = CharmmParameterSet(
get_fn("toppar_drude_master_protein_2013e.str"))
system = psf.createSystem(params)
def test_no_parameters(self):
""" Test proper error handling when parameters not present """
parm = CharmmPsfFile(get_fn('ala_ala_ala.psf'))
parm.rb_torsions.append(parm.dihedrals.pop())
parm.urey_bradleys.append(UreyBradley(parm.angles[0].atom1, parm.angles[0].atom3))
self.assertRaises(ParameterError, parm.omm_bond_force)
self.assertRaises(ParameterError, parm.omm_angle_force)
self.assertRaises(ParameterError, parm.omm_dihedral_force)
self.assertRaises(ParameterError, parm.omm_rb_torsion_force)
self.assertRaises(ParameterError, parm.omm_urey_bradley_force)
self.assertRaises(ParameterError, parm.omm_improper_force)
self.assertRaises(ParameterError, parm.omm_cmap_force)
def parse(filename):
""" Read a CHARMM- or XPLOR-style PSF file
Parameters
----------
filename : str
Name of the file to parse
Returns
-------
psf_file : :class:`CharmmPsfFile`
The PSF file instance with all information loaded
"""
return CharmmPsfFile(filename)
def test_turn_off_param(self):
""" Test turning off parameters """
structure = CharmmPsfFile(get_fn('butane_charge_off.psf'))
param = CharmmParameterSet(get_fn('par_all36_cgenff.prm'),
get_fn('top_all36_cgenff.rtf'))
par.turn_off_params(structure,
param,
bonds=True,
angles=True,
dihedral=True,
urey_bradley=True,
lj=True,
copy=False)
scan = get_fn('MP2_torsion_scan/')
butane_scan = qmdb.parse_psi4_out(scan,
get_fn('butane_charge_off.psf'))
butane_scan.compute_energy(param)
self.assertTrue((butane_scan.mm_energy.value_in_unit(
unit.kilojoule_per_mole) == 0).all())
def parse_psi4_log(logfiles, structure):
"""
Parses output of psi4 torsion scan script
:param logfiles: list of str
logfiles of psi4 script
:param structure: str
Charmm psf file of structure
:return:
TorsionScanSet
"""
topology = md.load_psf(structure)
structure = CharmmPsfFile(structure)
positions = np.ndarray((0, topology.n_atoms, 3))
qm_energies = np.ndarray(0)
torsions = np.ndarray((0, 4), dtype=int)
directions = np.ndarray(0, dtype=int)
angles = np.ndarray(0, dtype=float)
if type(logfiles) != list:
logfiles = [logfiles]
for file in logfiles:
qm = np.ndarray(0)
fi = open(file, 'r')
# check if log file is complete
complete = False # complete flag
for line in fi:
if line.startswith('Relative'):
complete = True
fi.seek(0)
section = None
torsion = np.ndarray((1, 4), dtype=int)
angle = np.ndarray(0, dtype=float)
for line in fi:
# Flag if structure is optimized
optimized = False
if line.startswith('Optimizer'):
optimized = True
# Store Dihedral and position of optimized structures
fi.next()
l = filter(None, fi.next().strip().split(' '))
dih = round(float(l[-2]))
try:
t = l[-6:-2]
for i in range(len(t)):
torsion[0][i] = int(t[i]) - 1
torsions = np.append(torsions, torsion, axis=0)
except ValueError:
pass
angle = np.append(angle, dih)
fi.next()
pos = filter(None, re.split("[, \[\]]", fi.next().strip()))
pos = [float(i) for i in pos]
pos = np.asarray(pos).reshape((-1, 3))
# convert angstroms to nanometers
positions = np.append(positions, pos[np.newaxis] * 0.1, axis=0)
if not complete and optimized:
# Find line that starts with energy
for line in fi:
if line.startswith('Energy'):
energy = filter(None, line.strip().split(' '))[-1]
# Convert to KJ/mol
energy = float(energy) * 2625.5
qm = np.append(qm, energy)
break
if line.startswith('Relative'):
section = 'Energy'
fi.next()
continue
if section == 'Energy':
line = filter(None, line.strip().split(' '))
if line != []:
dih = round(float(line[0]))
if dih in angle:
# Only save energies of optimized structures
qm_energies = np.append(qm_energies, float(line[-1]))
if qm.size is not 0:
qm = qm - min(qm)
qm_energies = np.append(qm_energies, qm)
fi.close()
angles = np.append(angles, angle, axis=0)
return QMDataBase(positions, topology, structure, torsions, directions,
angles, qm_energies)
def parse_gauss(logfiles, structure):
""" parses Guassian09 torsion-scan log file
parameters
----------
logfiles: str of list of str
Name of Guassian 09 torsion scan log file
structure: charmm psf file
returns
-------
TorsionScanSet
"""
topology = md.load_psf(structure)
structure = CharmmPsfFile(structure)
positions = np.ndarray((0, topology.n_atoms, 3))
qm_energies = np.ndarray(0)
torsions = np.ndarray((0, 4), dtype=int)
directions = np.ndarray(0, dtype=int)
steps = np.ndarray((0, 3), dtype=int)
if type(logfiles) != list:
logfiles = [logfiles]
for file in (logfiles):
direction = np.ndarray(1)
torsion = np.ndarray((1, 4), dtype=int)
step = np.ndarray((0, 3), dtype=int)
index = (2, 12, -1)
log = Gaussian(file)
data = log.parse()
# convert angstroms to nanometers
positions = np.append(positions, data.atomcoords * 0.1, axis=0)
# Only add qm energies for structures that converged (because cclib throws out those coords but not other info)
qm_energies = np.append(qm_energies, (convertor(
data.scfenergies[:len(data.atomcoords)], "eV", "kJmol-1") - min(
convertor(data.scfenergies[:len(data.atomcoords)], "eV",
"kJmol-1"))),
axis=0)
fi = open(file, 'r')
for line in fi:
if re.search(' Scan ', line):
t = line.split()[2].split(',')
t[0] = t[0][-1]
t[-1] = t[-1][0]
for i in range(len(t)):
torsion[0][i] = (int(t[i]) - 1)
if re.search('^ D ', line):
d = line.split()[-1]
if d[0] == '-':
direction[0] = 0
elif d[0] == '1':
direction[0] = 1
if re.search('Step', line):
try:
point = np.array(([int(line.rsplit()[j]) for j in index]))
point = point[np.newaxis, :]
step = np.append(step, point, axis=0)
except:
pass
fi.close()
# only add scan points from converged structures
steps = np.append(steps, step[:len(data.atomcoords)], axis=0)
for i in range(len(data.atomcoords)):
torsions = np.append(torsions, torsion, axis=0)
directions = np.append(directions, direction, axis=0)
del log
del data
return QMDataBase(positions=positions,
topology=topology,
structure=structure,
torsions=torsions,
steps=steps,
qm_energies=qm_energies,
directions=directions)
def parse_psi4_out(oufiles_dir, structure, pattern="*.out"):
"""
Parse psi4 out files from distributed torsion scan (there are many output files, one for each structure)
:param oufiles_dir: str
path to directory where the psi4 output files are
:param structure: str
path to psf, mol2 or pbd file of structure
:param pattern: str
pattern for psi4 output file. Default is *.out
:return: TorsionScanSet
"""
# Check extension of structure file
if structure.endswith('psf'):
topology = md.load_psf(structure)
structure = CharmmPsfFile(structure)
else:
topology = md.load(structure).topology
structure = parmed.load_file(structure)
positions = np.ndarray((0, topology.n_atoms, 3))
qm_energies = np.ndarray(0)
torsions = np.ndarray((0, 4), dtype=int)
angles = np.ndarray(0, dtype=float)
optimized = np.ndarray(0, dtype=bool)
out_files = {}
for path, subdir, files in os.walk(oufiles_dir):
for name in files:
if fnmatch(name, pattern):
if name.startswith('timer'):
continue
name_split = name.split('_')
try:
torsion_angle = (name_split[1] + '_' + name_split[2] +
'_' + name_split[3] + '_' + name_split[4])
except IndexError:
warnings.warn(
"Do you only have one torsion scan? The output files will be treated as one scan"
)
torsion_angle = 'only_one_scan'
try:
out_files[torsion_angle]
except KeyError:
out_files[torsion_angle] = []
path = os.path.join(os.getcwd(), path, name)
out_files[torsion_angle].append(path)
# Sort files in increasing angles order for each torsion
sorted_files = []
dih_angles = []
for tor in out_files:
dih_angle = []
for file in out_files[tor]:
dih_angle.append(int(file.split('_')[-1].split('.')[0]))
sorted_files.append([
out_file
for (angle, out_file) in sorted(zip(dih_angle, out_files[tor]))
])
dih_angle.sort()
dih_angles.append(dih_angle)
if not out_files:
raise Exception(
"There are no psi4 output files. Did you choose the right directory?"
)
# Parse files
for f in itertools.chain.from_iterable(sorted_files):
torsion = np.ndarray((1, 4), dtype=int)
fi = open(f, 'r')
for line in fi:
if line.startswith('dih_string'):
t = line.strip().split('"')[1].split(' ')[:4]
for i in range(len(t)):
torsion[0][i] = int(t[i]) - 1
torsions = np.append(torsions, torsion, axis=0)
fi.close()
optimizer = True
log = Psi(f)
data = log.parse()
try:
data.optdone
except AttributeError:
optimizer = False
warnings.warn("Warning: Optimizer failed for {}".format(f))
optimized = np.append(optimized, optimizer)
positions = np.append(positions,
data.atomcoords[-1][np.newaxis] * 0.1,
axis=0)
# Try MP2 energies. Otherwise take SCFenergies
try:
qm_energy = convertor(data.mpenergies[-1], "eV", "kJmol-1")
except AttributeError:
try:
qm_energy = convertor(np.array([data.scfenergies[-1]]), "eV",
"kJmol-1")
except AttributeError:
warnings.warn(
"Warning: Check if the file terminated before completing SCF"
)
qm_energy = np.array([np.nan])
qm_energies = np.append(qm_energies, qm_energy, axis=0)
# Subtract lowest energy to find relative energies
qm_energies = qm_energies - min(qm_energies)
angles = np.asarray(list(itertools.chain.from_iterable(dih_angles)))
return QMDataBase(positions=positions,
topology=topology,
structure=structure,
torsions=torsions,
angles=angles,
qm_energies=qm_energies,
optimized=optimized)
class ToyModel(object):
"""
Toy model of 4 carbons to test torsionfit
Attributes
----------
synthetic_energy: simtk.units.Quantity((n_increments), unit=kilojoule/mole)
true_value: parmed.topologyobjects.DihedralTypeList (the dihedral parameters used to calculate synthetic energy)
initital_value: parmed.topologyobjects.DihedralTypeList (dihedral parameters used to initialize pymc model)
torsion_scan: torsionfit.TorsionScanSet
model: torsionfit.TorsionFitModel
The default toy model has randomized true and initial dihedral parameters. This can be changed by passing a
parmed.topologyobjects.DihedralTypeList to true_value and/or initial_value when initializing a model instance.
"""
def __init__(self, true_value=None, initial_value=None, n_increments=18, rj=True, sample_phase=False,
continuous=False):
self._param = CharmmParameterSet(get_fun('toy.str'))
self._struct = CharmmPsfFile(get_fun('toy.psf'))
self._pdb = app.PDBFile(get_fun('toy.pdb'))
self._topology = md.load_psf(get_fun('toy.psf'))
self.synthetic_energy = units.Quantity()
self._positions = units.Quantity()
self._platform = mm.Platform.getPlatformByName('Reference')
# Replace ('CG331', 'CG321', 'CG321', 'CG331') torsion with true_value
self._dih_type = ('CG331', 'CG321', 'CG321', 'CG331')
original_torsion = self._param.dihedral_types[self._dih_type]
if true_value is not None:
if type(true_value) == DihedralTypeList:
dih_tlist = true_value
elif type(true_value) == DihedralType:
dih_tlist = DihedralTypeList()
dih_tlist.append(true_value)
else:
dih_tlist = self._randomize_dih_param(return_dih=True)
self.true_value = copy.deepcopy(dih_tlist)
self._param.dihedral_types[self._dih_type] = dih_tlist
# parametrize toy
self._struct.load_parameters(self._param, copy_parameters=False)
self._struct.positions = self._pdb.positions
# generate synthetic torsion scan
self._torsion_scan(n_increments=n_increments)
# initialize parameter
if initial_value is not None:
if type(initial_value) == DihedralTypeList:
dih_tlist = initial_value
if type(initial_value) == DihedralType:
dih_tlist = DihedralTypeList()
dih_tlist.append(initial_value)
elif initial_value == 'cgenff':
dih_tlist = original_torsion
else:
dih_tlist = self._randomize_dih_param(return_dih=True)
self.initial_value = copy.deepcopy(dih_tlist)
self._param.dihedral_types[self._dih_type] = dih_tlist
# create torsionfit.TorsionScanSet
torsions = np.zeros((len(self._positions), 4))
torsions[:] = [1, 2, 3, 4]
direction = None
steps = None
self.scan_set = ScanSet.QMDataBase(positions=self._positions.value_in_unit(units.nanometers),
topology=self._topology, structure=self._struct, torsions=torsions,
steps=steps, directions=direction,
qm_energies=self.synthetic_energy.value_in_unit(units.kilojoules_per_mole))
self.model = model.TorsionFitModel(param=self._param, frags=self.scan_set, platform=self._platform,
param_to_opt=[self._dih_type], rj=rj, continuous_phase=continuous,
sample_phase=sample_phase)
def _spher2cart(self, r, theta, phi):
"""convert spherical to cartesian coordinates
Paramters:
r: bond length
theta: bond angle
phi: dihedral angle
returns:
cartesian coordinates
"""
x = r * np.sin(theta) * np.cos(phi)
y = r * np.sin(theta) * np.sin(phi)
z = r * np.cos(theta)
return [x, y, z]
def _torsion_scan(self, n_increments):
"""
Generate positions and energy for torsion scan
Parameters:
n_increments: int. how many points to scan
"""
n_increments = n_increments
n_atoms = 4
phis = np.arange(-np.pi, +np.pi, np.pi/n_increments)
positions = np.zeros((len(phis), n_atoms, 3))
# Get bond length in nm
for bond in self._struct.bonds:
if bond.atom1.type == bond.atom2.type:
length = units.Quantity(value=bond.type.req * 0.1, unit=units.nanometers) # convert to nm
# Get angle in radians
for angle in self._struct.angles:
if angle.atom1.type == angle.atom2.type:
theta = units.Quantity(value=angle.type.theteq * (np.pi/180.0), unit=units.radians)
atom1_coords = self._spher2cart(length.value_in_unit(units.nanometer), theta.value_in_unit(units.radian), phis[0])
for i, phi in enumerate(phis):
atom3_coords = self._spher2cart(length.value_in_unit(units.nanometer), theta.value_in_unit(units.radian), phi)
atom3_coords[-1] = abs(atom3_coords[-1]) + length._value
positions[i] = [atom1_coords,
[0.000, 0.000, 0.000],
[0.000, 0.000, length._value],
atom3_coords]
self._positions = units.Quantity(value=positions, unit=units.nanometer) # put units back in
# calculate energy
self.synthetic_energy = units.Quantity(value=np.zeros((len(positions))), unit=units.kilojoules_per_mole)
platform = mm.Platform.getPlatformByName('Reference')
integrator = mm.VerletIntegrator(0.004*units.picoseconds)
system = self._struct.createSystem()
context = mm.Context(system, integrator, platform)
for i, conf in enumerate(self._positions):
context.setPositions(conf)
state = context.getState(getEnergy=True)
energy = state.getPotentialEnergy()
self.synthetic_energy[i] = energy + units.Quantity(value=np.random.normal(0, 1.0), unit=units.kilojoules_per_mole)
def _randomize_dih_param(self, return_dih=False):
"""
generates random dihedral parameters
"""
dih_tlist = DihedralTypeList()
multiplicities = [1, 2, 3, 4, 6]
terms = np.random.randint(1, 5+1)
np.random.shuffle(multiplicities)
for i in range(terms):
k = np.random.uniform(0.0, 20.0)
n = multiplicities[i]
phase = np.random.randint(0, 1+1)
if phase == 1:
phase = 180
dih_tlist.append(DihedralType(k, n, phase, 1.00, 1.00))
self._param.dihedral_types[self._dih_type] = dih_tlist
if return_dih:
_dih_tlist = copy.deepcopy(dih_tlist)
return _dih_tlist
def save_torsion_values(self, filename=None):
"""
Parameters
----------
filename : str
file to save torsion values. Default is None. If None, return np.array
Returns
-------
dih_param: np.array
array containing torison parameters
"""
dih_param = np.ones(shape=(2, 6, 3)) * np.nan
for i, dih in enumerate(self.true_value):
dih_param[0, i, 0] = dih.per
dih_param[0, i, 1] = dih.phi_k
dih_param[0, i, 2] = dih.phase
for j, dih in enumerate(self.initial_value):
dih_param[1, j, 0] = dih.per
dih_param[1, j, 1] = dih.phi_k
dih_param[1, j, 2] = dih.phase
if filename is not None:
np.save(filename, dih_param)
else:
return dih_param
@staticmethod
def from_dih_params(filename=None, dih_params=None, rj=False, continuous=False, n_increments=13, sample_phase=False):
"""
Parameters
----------
filename : str
name of file with serialized dihedral parameters
rj : bool
Flag if using reversible jump. Default it True
continuous : bool
Flag if sampling continuous phase. Default is False
n_increments : int
incermentation of torsion drive
sample_phase : bool
Flag if sampling phase. Default is False (K is allowed to go negative when sample_phase is False)
Returns
-------
ToyModel with true and initial value from saved file.
"""
if filename is None and dih_params is None:
msg = 'You must provide either an npy file or a numpy array with true and initial values for the toy model'
raise Exception(msg)
if filename is not None:
dih_params = np.load(filename)
dih_tlist_true = DihedralTypeList()
dih_tlist_init = DihedralTypeList()
true = dih_params[0]
init = dih_params[1]
for dih in true:
if not np.isnan(dih[0]):
dih_tlist_true.append(DihedralType(per=dih[0], phi_k=dih[1], phase=dih[2]))
for dih in init:
if not np.isnan(dih[0]):
dih_tlist_init.append(DihedralType(per=dih[0], phi_k=dih[1], phase=dih[2]))
return ToyModel(true_value=dih_tlist_true, initial_value=dih_tlist_init, rj=rj, continuous=continuous,
n_increments=n_increments, sample_phase=sample_phase)
pdb_solvate = app.PDBFile('../structure/butane_solvated.pdb')
coords = pdb_solvate.positions
min_crds = [coords[0][0], coords[0][1], coords[0][2]]
max_crds = [coords[0][0], coords[0][1], coords[0][2]]
for coord in coords:
min_crds[0] = min(min_crds[0], coord[0])
min_crds[1] = min(min_crds[1], coord[1])
min_crds[2] = min(min_crds[2], coord[2])
max_crds[0] = max(max_crds[0], coord[0])
max_crds[1] = max(max_crds[1], coord[1])
max_crds[2] = max(max_crds[2], coord[2])
psf_solvate_1 = CharmmPsfFile('../structure/butane_solvated.psf')
psf_solvate_1.box = (max_crds[0] - min_crds[0], max_crds[1] - min_crds[1],
max_crds[2] - min_crds[2], 90.0, 90.0, 90.0)
database['solvated']['structure_1'] = psf_solvate_1
psf_solvate_1.load_parameters(param_1, copy_parameters=False)
system_solvate_1 = psf_solvate_1.createSystem(
nonbondedMethod=app.PME,
constraints=app.HBonds,
nonbondedCutoff=12.0 * u.angstroms,
switchDistance=10.0 * u.angstroms)
database['solvated']['system_1'] = system_solvate_1
psf_solvate_2 = CharmmPsfFile('../structure/butane_solvated.psf')
psf_solvate_2.box = (max_crds[0] - min_crds[0], max_crds[1] - min_crds[1],
max_crds[2] - min_crds[2], 90.0, 90.0, 90.0)
database['solvated']['structure_2'] = psf_solvate_2
def compare_energies(system_name,
pdb_filename,
psf_filename,
ffxml_filenames,
toppar_filenames,
box_vectors_filename=None,
system_kwargs=None,
tolerance=1e-5,
units=u.kilojoules_per_mole,
write_serialized_xml=False):
"""
Compare energies between (pdb, psf, toppar) loaded via ParmEd and (pdb, ffxml) loaded by OpenMM ForceField
Parameters
----------
system_name : str
Name of the test system
pdb_filename : str
Name of PDB file that should contain CRYST entry and PDB format compliant CONECT records for HETATM residues.
psf_filename : str
CHARMM PSF file
ffxml_filenames : list of str
List of OpenMM ffxml files
toppar_filenames : list of CHARMM toppar filenames to load into CharmmParameterSet
List of CHARMM toppar files
box_vectors_filename : str, optional, default=None
If specified, read box vectors from a file like step2.1_waterbox.prm
system_kwargs : dict, optional, default=None
Keyword arguments to pass to CharmmPsfFile.createSystem() and ForceField.CreateSystem() when constructing System objects for energy comparison
tolerance : float, optional, default=1e-5
Relative energy discrepancy tolerance
units : simtk.unit.Unit
Unit to use for energy comparison
write_serialized_xml : bool, optional, default=False
If True, will write out serialized System XML files for OpenMM systems to aid debugging.
"""
is_periodic = False
if (system_kwargs is not None) and ('nonbondedMethod'
in system_kwargs) and (
system_kwargs['nonbondedMethod']
in [app.CutoffPeriodic, app.PME]):
is_periodic = True
# Load PDB file
pdbfile = app.PDBFile(pdb_filename)
# Read box vectors
if box_vectors_filename:
box_vectors = read_box_vectors(box_vectors_filename)
pdbfile.topology.setPeriodicBoxVectors(box_vectors)
else:
box_vectors = pdbfile.topology.getPeriodicBoxVectors()
# Load CHARMM system through OpenMM
openmm_toppar = app.CharmmParameterSet(*toppar_filenames)
openmm_psf = app.CharmmPsfFile(psf_filename)
# Set box vectors
if is_periodic:
openmm_psf.setBox(box_vectors[0][0], box_vectors[1][1],
box_vectors[2][2])
openmm_system = openmm_psf.createSystem(openmm_toppar, **system_kwargs)
openmm_structure = openmm.load_topology(openmm_psf.topology,
openmm_system,
xyz=pdbfile.positions)
#openmm_energies = openmm.energy_decomposition_system(openmm_structure, openmm_system, nrg=units)
#print('OpenMM CHARMM loader energy components : %s' % str(openmm_energies))
openmm_total_energy = compute_potential(openmm_system,
pdbfile.positions) / units
# Load CHARMM system through ParmEd
parmed_toppar = CharmmParameterSet(*toppar_filenames)
parmed_structure = CharmmPsfFile(psf_filename)
#structure.load_parameters(toppar)
parmed_structure.positions = pdbfile.positions
# Set box vectors
if is_periodic:
parmed_structure.box = (box_vectors[0][0] / u.angstroms,
box_vectors[1][1] / u.angstroms,
box_vectors[2][2] / u.angstroms, 90, 90, 90)
parmed_system = parmed_structure.createSystem(parmed_toppar,
**system_kwargs)
#parmed_energies = openmm.energy_decomposition_system(parmed_structure, parmed_system, nrg=units)
#print('ParmEd CHARMM loader energy components : %s' % str(parmed_energies))
parmed_total_energy = compute_potential(parmed_system,
pdbfile.positions) / units
# Delete H-H bonds from waters and retreive updated topology and positions
modeller = app.Modeller(openmm_psf.topology, pdbfile.positions)
hhbonds = [
b for b in modeller.topology.bonds()
if b[0].element == app.element.hydrogen
and b[1].element == app.element.hydrogen
]
modeller.delete(hhbonds)
ffxml_topology = modeller.topology
# OpenMM system with ffxml
ff = app.ForceField(*ffxml_filenames)
ffxml_system = ff.createSystem(ffxml_topology, **system_kwargs)
ffxml_structure = openmm.load_topology(ffxml_topology,
ffxml_system,
xyz=pdbfile.positions)
#ffxml_energies = openmm.energy_decomposition_system(ffxml_structure, ffxml_system, nrg=units)
#print('ffxml energy components : %s' % str(ffxml_energies))
ffxml_total_energy = compute_potential(ffxml_system,
pdbfile.positions) / units
write_serialized_xml = True # DEBUG
if write_serialized_xml:
print('Writing serialized XML files...')
write_serialized_system(system_name + '.charmm.system.xml',
openmm_system)
write_serialized_system(system_name + '.parmed.system.xml',
parmed_system)
write_serialized_system(system_name + '.openmm.system.xml',
ffxml_system)
print('-' * 100)
print('')
print('OpenMM CHARMM reader total energy: %14.3f' % openmm_total_energy)
print('ParmEd CHARMM reader total energy: %14.3f' % parmed_total_energy)
print('OPENMM ffxml total energy: %14.3f' % ffxml_total_energy)
print('TOTAL ERROR: %14.3f' %
(ffxml_total_energy - openmm_total_energy))
print('')
print('-' * 100)
# TODO : Automate comparison
return
# calc rel energies and assert
rel_energies = []
for i, j in zip(ffxml_energies, parmed_energies):
if i[0] != j[0]:
raise Exception('Mismatch in energy tuples naming.')
if abs(i[1]) > NEARLYZERO:
rel_energies.append((i[0], abs((i[1] - j[1]) / i[1])))
else:
if abs(j[1]) > NEARLYZERO:
raise AssertionError(
'One of the CHARMM %s energies (%s) for %s is zero, '
'while the corresponding OpenMM energy is non-zero' %
(system_name, i[0], ffxml))
rel_energies.append((i[0], 0))
dihedrals_done = False
for i in rel_energies:
if i[0] != 'PeriodicTorsionForce':
if i[1] > tolerance:
raise AssertionError(
'%s energies (%s, %f) outside of allowed tolerance (%f) for %s'
% (system_name, i[0], i[1], tolerance, ffxml))
else:
if not dihedrals_done:
if i[1] > tolerance:
raise AssertionError(
'%s energies (%s, %f) outside of allowed tolerance (%f) for %s'
% (system_name, i[0], i[1], tolerance, ffxml))
dihedrals_done = True
else: #impropers
if i[1] > improper_tolerance:
raise AssertionError(
'%s energies (%s-impropers, %f) outside of allowed tolerance (%f) for %s'
% (system_name, i[0], i[1], improper_tolerance, ffxml))
# logging
if not no_log:
charmm_energies_log = dict()
omm_energies_log = dict()
rel_energies_log = dict()
charmm_energies_log['ffxml_name'] = ffxml
charmm_energies_log['test_system'] = system_name
charmm_energies_log['data_type'] = 'CHARMM'
charmm_energies_log['units'] = units
omm_energies_log['ffxml_name'] = ffxml
omm_energies_log['test_system'] = system_name
omm_energies_log['data_type'] = 'OpenMM'
omm_energies_log['units'] = units
rel_energies_log['ffxml_name'] = ffxml
rel_energies_log['test_system'] = system_name
rel_energies_log['data_type'] = 'abs((CHARMM-OpenMM)/CHARMM)'
dihedrals_done = False
for item in amber_energies:
if item[0] == 'PeriodicTorsionForce' and not dihedrals_done:
charmm_energies_log['PeriodicTorsionForce_dihedrals'] = item[1]
dihedrals_done = True
elif item[0] == 'PeriodicTorsionForce' and dihedrals_done:
charmm_energies_log['PeriodicTorsionForce_impropers'] = item[1]
elif item[0] == 'CMMotionRemover':
continue
else:
charmm_energies_log[item[0]] = item[1]
dihedrals_done = False
for item in omm_energies:
if item[0] == 'PeriodicTorsionForce' and not dihedrals_done:
omm_energies_log['PeriodicTorsionForce_dihedrals'] = item[1]
dihedrals_done = True
elif item[0] == 'PeriodicTorsionForce' and dihedrals_done:
omm_energies_log['PeriodicTorsionForce_impropers'] = item[1]
elif item[0] == 'CMMotionRemover':
continue
else:
omm_energies_log[item[0]] = item[1]
dihedrals_done = False
for item in rel_energies:
if item[0] == 'PeriodicTorsionForce' and not dihedrals_done:
rel_energies_log['PeriodicTorsionForce_dihedrals'] = item[1]
dihedrals_done = True
elif item[0] == 'PeriodicTorsionForce' and dihedrals_done:
rel_energies_log['PeriodicTorsionForce_impropers'] = item[1]
elif item[0] == 'CMMotionRemover':
continue
else:
rel_energies_log[item[0]] = item[1]
logger.log(charmm_energies_log)
logger.log(omm_energies_log)
logger.log(rel_energies_log)
from __future__ import division, print_function
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
# ParmEd Imports
from parmed.charmm import CharmmPsfFile, CharmmCrdFile, CharmmParameterSet
from parmed.openmm import StateDataReporter
from parmed import unit as u
# Load the CHARMM files
print('Loading CHARMM files...')
params = CharmmParameterSet('BNZ_2_PRD.prm')
ala5_gas = CharmmPsfFile('zero.psf')
ala5_crds = app.PDBFile('A2B_gas.pdb')
CharmmParameterSet)
from parmed.exceptions import CharmmWarning, ParameterError
from parmed.openmm.utils import energy_decomposition
from parmed import unit as u, openmm, load_file, UreyBradley
from parmed.utils.six.moves import range
from copy import copy
from math import sqrt
import unittest
from utils import get_fn, TestCaseRelative, mm, app, has_openmm, CPU, Reference
import warnings
# Suppress warning output from bad psf file... sigh.
warnings.filterwarnings('ignore', category=CharmmWarning)
# System
charmm_gas = CharmmPsfFile(get_fn('ala_ala_ala.psf'))
charmm_gas_crds = load_file(get_fn('ala_ala_ala.pdb'))
charmm_nbfix = CharmmPsfFile(get_fn('ala3_solv.psf'))
charmm_nbfix_crds = CharmmCrdFile(get_fn('ala3_solv.crd'))
charmm_nbfix.box = [3.271195e1, 3.299596e1, 3.300715e1, 90, 90, 90]
# Parameter sets
param22 = CharmmParameterSet(get_fn('top_all22_prot.inp'),
get_fn('par_all22_prot.inp'))
param36 = CharmmParameterSet(get_fn('par_all36_prot.prm'),
get_fn('toppar_water_ions.str'))
@unittest.skipUnless(has_openmm, "Cannot test without OpenMM")
class TestCharmmFiles(TestCaseRelative):
def test_gas_energy(self):
from parmed.openmm.utils import energy_decomposition
from parmed import unit as u, openmm, load_file
from parmed.utils.six.moves import range
from copy import copy
from math import sqrt
import unittest
from utils import get_fn, TestCaseRelative, mm, app, has_openmm, CPU, Reference
import warnings
# Suppress warning output from bad psf file... sigh.
warnings.filterwarnings('ignore', category=CharmmWarning)
# System
charmm_gas = CharmmPsfFile(get_fn('ala_ala_ala.psf'))
charmm_gas_crds = load_file(get_fn('ala_ala_ala.pdb'))
charmm_nbfix = CharmmPsfFile(get_fn('ala3_solv.psf'))
charmm_nbfix_crds = CharmmCrdFile(get_fn('ala3_solv.crd'))
charmm_nbfix.box = [3.271195e1, 3.299596e1, 3.300715e1, 90, 90, 90]
# Parameter sets
param22 = CharmmParameterSet(get_fn('top_all22_prot.inp'),
get_fn('par_all22_prot.inp'))
param36 = CharmmParameterSet(get_fn('par_all36_prot.prm'),
get_fn('toppar_water_ions.str'))
@unittest.skipUnless(has_openmm, "Cannot test without OpenMM")
class TestCharmmFiles(TestCaseRelative):
def testGasEnergy(self):
""" Compare OpenMM and CHARMM gas phase energies """
parm = charmm_gas
import parmed as pm
from parmed.charmm import CharmmPsfFile, CharmmCrdFile, CharmmParameterSet
print('Loading CHARMM files...')
params = CharmmParameterSet('toppar/par_all36m_prot.prm', 'toppar/par_all36_lipid.prm')
gram = CharmmPsfFile('../../simulations/themis_data/1jnoetaohh3o2.psf')
for atom in gram.atoms:
print(atom.name, atom.idx, atom.charge, atom.rmin, atom.epsilon)