def _topology_from_residue(res):
"""Converts a openmm.app.Topology.Residue to openmm.app.Topology.
Parameters
----------
res : openmm.app.Topology.Residue
An individual residue in an openmm.app.Topology
Returns
-------
topology : openmm.app.Topology
The generated topology
"""
topology = app.Topology()
chain = topology.addChain()
new_res = topology.addResidue(res.name, chain)
atoms = dict() # { omm.Atom in res : omm.Atom in *new* topology }
for res_atom in res.atoms():
topology_atom = topology.addAtom(name=res_atom.name,
element=res_atom.element,
residue=new_res)
atoms[res_atom] = topology_atom
topology_atom.bond_partners = []
for bond in res.bonds():
atom1 = atoms[bond.atom1]
atom2 = atoms[bond.atom2]
topology.addBond(atom1, atom2)
atom1.bond_partners.append(atom2)
atom2.bond_partners.append(atom1)
return topology
def build_water_system(box_width):
ff = app.ForceField('tip3p.xml')
# Create empty topology and coordinates.
top = app.Topology()
pos = unit.Quantity((), unit.angstroms)
m = app.Modeller(top, pos)
boxSize = Vec3(box_width, box_width, box_width)*unit.nanometers
m.addSolvent(ff, boxSize=boxSize, model='tip3p')
system = ff.createSystem(
m.getTopology(),
nonbondedMethod=app.NoCutoff,
constraints=None,
rigidWater=False
)
positions = m.getPositions()
positions = unit.Quantity(np.array(positions / positions.unit), positions.unit)
assert m.getTopology().getNumAtoms() == positions.shape[0]
# TODO: minimize the water box (BFGS or scipy.optimize)
return system, positions, np.eye(3)*box_width, m.getTopology()
def _build_new_topology(current_receptor_topology, oemol_proposed):
"""
Construct a new topology
Parameters
----------
oemol_proposed : oechem.OEMol object
the proposed OEMol object
current_receptor_topology : app.Topology object
The current topology without the small molecule
Returns
-------
new_topology : app.Topology object
A topology with the receptor and the proposed oemol
mol_start_index : int
The first index of the small molecule
"""
oemol_proposed.SetTitle("MOL")
mol_topology = forcefield_generators.generateTopologyFromOEMol(
oemol_proposed)
new_topology = app.Topology()
append_topology(new_topology, current_receptor_topology)
append_topology(new_topology, mol_topology)
# Copy periodic box vectors.
if current_receptor_topology._periodicBoxVectors != None:
new_topology._periodicBoxVectors = copy.deepcopy(
current_receptor_topology._periodicBoxVectors)
return new_topology
def _topology_from_parmed(structure, non_element_types):
"""Convert a ParmEd Structure to an OpenMM Topology. """
topology = app.Topology()
chain = topology.addChain()
residue = topology.addResidue(structure.title, chain)
atoms = dict() # pmd.Atom: omm.Atom
for pmd_atom in structure.atoms:
name = pmd_atom.name
if pmd_atom.element in non_element_types:
element = non_element_types[pmd_atom.element]
else:
if (isinstance(pmd_atom.atomic_number, int) and
pmd_atom.atomic_number != 0):
element = elem.Element.getByAtomicNumber(pmd_atom.atomic_number)
else:
element = elem.Element.getBySymbol(pmd_atom.name)
omm_atom = topology.addAtom(name, element, residue)
atoms[pmd_atom] = omm_atom
omm_atom.bond_partners = []
for bond in structure.bonds:
atom1 = atoms[bond.atom1]
atom2 = atoms[bond.atom2]
topology.addBond(atom1, atom2)
atom1.bond_partners.append(atom2)
atom2.bond_partners.append(atom1)
if structure.box_vectors and np.any([x._value for x in structure.box_vectors]):
topology.setPeriodicBoxVectors(structure.box_vectors)
positions = structure.positions
return topology, positions
def mol_to_topology(mol):
""" Create an openmm topology object from an MDT molecule
Args:
mol (moldesign.Molecule): molecule to copy topology from
Returns:
simtk.openmm.app.Topology: topology of the molecule
"""
from simtk.openmm import app
top = app.Topology()
chainmap = {chain: top.addChain(chain.name) for chain in mol.chains}
resmap = {
res: top.addResidue(res.resname, chainmap[res.chain],
str(res.pdbindex))
for res in mol.residues
}
atommap = {
atom: top.addAtom(atom.name,
app.Element.getBySymbol(atom.element),
resmap[atom.residue],
id=str(atom.pdbindex))
for atom in mol.atoms
}
for bond in mol.bonds:
top.addBond(atommap[bond.a1], atommap[bond.a2])
return top
def convert_spce_to_cs(file, saveas="newpdb.pdb"):
"""Extract and rename oxygens from all-atom water structure"""
import os
import numpy as np
import simtk.unit as unit
import simtk.openmm as omm
import simtk.openmm.app as app
file = "equil_spc.pdb"
saveas = "justO_spc.pdb"
app.element.solvent = app.element.Element(201, "Solvent", "Sv",
18 * unit.amu)
pdb = app.PDBFile(file)
O_idxs = np.array(
[atm.index for atm in pdb.topology.atoms() if atm.name == "O"])
xyz = np.array(pdb.positions / unit.angstrom)[O_idxs]
positions = unit.Quantity(xyz, unit.angstrom)
n_slv = len(O_idxs)
topology = app.Topology()
chain = topology.addChain()
for i in range(n_slv):
res = topology.addResidue("SLV", chain)
topology.addAtom("CS", app.element.get_by_symbol("Sv"), res)
box_edge = 5.96256971 * unit.nanometer
topology.setUnitCellDimensions(box_edge * omm.Vec3(1, 1, 1))
with open(saveas, "w") as fout:
pdb.writeFile(topology, positions, file=fout)
def to_omm_topology(self):
'''
Generate OpenMM topology from this topology
Returns
-------
omm_topology : mm.app.Topology
'''
try:
from simtk.openmm import app as omm_app
from simtk.openmm.app.element import Element as omm_Element
except ImportError:
raise Exception('cannot import openmm')
omm_top = omm_app.Topology()
omm_chain = omm_top.addChain()
for mol in self._molecules:
omm_residue = omm_top.addResidue(mol.name, omm_chain)
for atom in mol.atoms:
try:
omm_element = omm_Element.getBySymbol(atom.symbol)
except:
omm_element = None
omm_top.addAtom(atom.name, omm_element, omm_residue)
if self.cell.volume != 0:
omm_top.setPeriodicBoxVectors(self.cell.vectors)
omm_atoms = list(omm_top.atoms())
for bond in self.bonds:
omm_top.addBond(omm_atoms[bond.atom1.id], omm_atoms[bond.atom2.id])
return omm_top
def _create_torsion_sim(periodicity: int = 2,
phase=0 * omm_angle_unit,
k=10.0 * omm_energy_unit) -> app.Simulation:
"""Create a 4-particle OpenMM Simulation containing only a PeriodicTorsionForce"""
system = mm.System()
# add 4 particles of unit mass
for _ in range(4):
system.addParticle(1)
# add torsion force to system
force = mm.PeriodicTorsionForce()
force.addTorsion(0, 1, 2, 3, periodicity, phase, k)
system.addForce(force)
# create openmm Simulation, which requires a Topology and Integrator
topology = app.Topology()
chain = topology.addChain()
residue = topology.addResidue("torsion", chain)
for name in ["a", "b", "c", "d"]:
topology.addAtom(name, "C", residue)
integrator = mm.VerletIntegrator(1.0)
sim = app.Simulation(topology, system, integrator)
return sim
def create_omm_topology(self):
topology = app.Topology()
for molecule_name, number_of_molecule_copies in self.molecules:
for _ in range(number_of_molecule_copies):
self.add_moltype_to_omm_topology(
self.molecule_types[molecule_name],
topology,
)
return topology
def write_solvent_pdb(sigma_slv,
packing_fraction,
box_edge,
starting_pdb,
dummypdb="dum.pdb"):
"""Create solvent in box"""
# generate solvent
n_slv = int(round(packing_fraction * ((box_edge / sigma_slv)**3)))
xyz_slv = np.random.uniform(high=box_edge / unit.angstroms,
size=[n_slv, 3])
overlap_radius = sigma_slv / unit.angstrom
box_ang = box_edge / unit.angstrom
new_xyz_slv = []
for i in range(len(xyz_slv)):
not_overlapping = True
if i < (len(xyz_slv) - 1):
for n in range(i + 1, len(xyz_slv)):
sep = periodic_distance(xyz_slv[i], xyz_slv[n], box_ang)
if sep < overlap_radius:
# remove solvent that is overlapping itself
not_overlapping = False
break
if not_overlapping:
new_xyz_slv.append(xyz_slv[i])
xyz_slv = np.array(new_xyz_slv)
n_slv = len(xyz_slv)
# create topology
topology = app.Topology()
chain = topology.addChain()
for i in range(n_slv):
res = topology.addResidue("SLV", chain)
topology.addAtom("SV", app.element.get_by_symbol("Sv"), res)
positions = unit.Quantity(xyz_slv, unit.angstrom)
topology.setUnitCellDimensions(
(box_edge / unit.nanometer) * omm.Vec3(1, 1, 1))
pdb = app.PDBFile(dummypdb)
with open(starting_pdb, "w") as fout:
pdb.writeFile(topology, positions, file=fout)
def chimera_molecule_to_openmm_topology(*molecules):
"""
Convert a Chimera Molecule object to OpenMM structure,
providing topology and coordinates.
Parameters
----------
molecule : chimera.Molecule
Returns
-------
topology : simtk.openmm.app.topology.Topology
coordinates : simtk.unit.Quantity
"""
# Create topology
atoms, residues, chains = {}, {}, {}
topology = openmm_app.Topology()
for i, mol in enumerate(molecules):
for a in mol.atoms:
chain_id = (i, a.residue.id.chainId)
try:
chain = chains[chain_id]
except KeyError:
chain = chains[chain_id] = topology.addChain()
r = a.residue
try:
residue = residues[r]
except KeyError:
residue = residues[r] = topology.addResidue(r.type, chain)
name = a.name
element = openmm_app.Element.getByAtomicNumber(
a.element.number)
serial = a.serialNumber
atoms[a] = topology.addAtom(name, element, residue, serial)
for b in mol.bonds:
topology.addBond(atoms[b.atoms[0]], atoms[b.atoms[1]])
return topology
def save_coords(saveas, xyz_ply, box_edge_nm):
# create polymer topology
topology = app.Topology()
chain = topology.addChain()
for i in range(len(xyz_ply)):
res = topology.addResidue("PLY", chain)
atm = topology.addAtom("PL", app.element.get_by_symbol("Pl"), res)
if i == 0:
prev_atm = atm
else:
topology.addBond(prev_atm, atm)
prev_atm = atm
positions = unit.Quantity(xyz_ply, unit.nanometer)
topology.setUnitCellDimensions(box_edge_nm * omm.Vec3(1, 1, 1))
pdb = app.PDBFile("dum.pdb")
with open(saveas, "w") as fout:
pdb.writeFile(topology, positions, file=fout)
def test_mutate_from_every_amino_to_every_other():
"""
Make sure mutations are successful between every possible pair of before-and-after residues
Mutate Ecoli F-ATPase alpha subunit to all 20 amino acids (test going FROM all possibilities)
Mutate each residue to all 19 alternatives
"""
import perses.rjmc.topology_proposal as topology_proposal
aminos = [
'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE',
'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL'
]
failed_mutants = 0
pdbid = "2A7U"
topology, positions = load_pdbid_to_openmm(pdbid)
modeller = app.Modeller(topology, positions)
for chain in modeller.topology.chains():
pass
modeller.delete([chain])
ff_filename = "amber99sbildn.xml"
max_point_mutants = 1
ff = app.ForceField(ff_filename)
system = ff.createSystem(modeller.topology)
chain_id = 'A'
metadata = dict()
system_generator = topology_proposal.SystemGenerator([ff_filename])
pm_top_engine = topology_proposal.PointMutationEngine(
modeller.topology,
system_generator,
chain_id,
proposal_metadata=metadata,
max_point_mutants=max_point_mutants,
always_change=True)
current_system = system
current_topology = modeller.topology
current_positions = modeller.positions
pm_top_engine._allowed_mutations = list()
for k, proposed_amino in enumerate(aminos):
pm_top_engine._allowed_mutations.append((str(k + 2), proposed_amino))
pm_top_proposal = pm_top_engine.propose(current_system, current_topology)
current_system = pm_top_proposal.new_system
current_topology = pm_top_proposal.new_topology
for chain in current_topology.chains():
if chain.id == chain_id:
# num_residues : int
num_residues = len(chain._residues)
break
new_sequence = list()
for residue in current_topology.residues():
if residue.index == 0:
continue
if residue.index == (num_residues - 1):
continue
if residue.name in ['HID', 'HIE']:
residue.name = 'HIS'
new_sequence.append(residue.name)
for i in range(len(aminos)):
assert new_sequence[i] == aminos[i]
pm_top_engine = topology_proposal.PointMutationEngine(
current_topology,
system_generator,
chain_id,
proposal_metadata=metadata,
max_point_mutants=max_point_mutants)
from perses.rjmc.topology_proposal import append_topology
old_topology = app.Topology()
append_topology(old_topology, current_topology)
new_topology = app.Topology()
append_topology(new_topology, current_topology)
old_chemical_state_key = pm_top_engine.compute_state_key(old_topology)
for chain in new_topology.chains():
if chain.id == chain_id:
# num_residues : int
num_residues = len(chain._residues)
break
for proposed_location in range(1, num_residues - 1):
print('Making mutations at residue %s' % proposed_location)
original_residue_name = chain._residues[proposed_location].name
matching_amino_found = 0
for proposed_amino in aminos:
pm_top_engine._allowed_mutations = [(str(proposed_location + 1),
proposed_amino)]
new_topology = app.Topology()
append_topology(new_topology, current_topology)
old_system = current_system
old_topology_natoms = sum([1 for atom in old_topology.atoms()])
old_system_natoms = old_system.getNumParticles()
if old_topology_natoms != old_system_natoms:
msg = 'PolymerProposalEngine: old_topology has %d atoms, while old_system has %d atoms' % (
old_topology_natoms, old_system_natoms)
raise Exception(msg)
metadata = dict()
for atom in new_topology.atoms():
atom.old_index = atom.index
index_to_new_residues, metadata = pm_top_engine._choose_mutant(
new_topology, metadata)
if len(index_to_new_residues) == 0:
matching_amino_found += 1
continue
print('Mutating %s to %s' %
(original_residue_name, proposed_amino))
residue_map = pm_top_engine._generate_residue_map(
new_topology, index_to_new_residues)
for res_pair in residue_map:
residue = res_pair[0]
name = res_pair[1]
assert residue.index in index_to_new_residues.keys()
assert index_to_new_residues[residue.index] == name
assert residue.name + '-' + str(
residue.id) + '-' + name in metadata['mutations']
new_topology, missing_atoms = pm_top_engine._delete_excess_atoms(
new_topology, residue_map)
new_topology = pm_top_engine._add_new_atoms(
new_topology, missing_atoms, residue_map)
for res_pair in residue_map:
residue = res_pair[0]
name = res_pair[1]
assert residue.name == name
atom_map = pm_top_engine._construct_atom_map(
residue_map, old_topology, index_to_new_residues, new_topology)
templates = pm_top_engine._ff.getMatchingTemplates(new_topology)
assert [
templates[index].name == residue.name
for index, (residue, name) in enumerate(residue_map)
]
new_chemical_state_key = pm_top_engine.compute_state_key(
new_topology)
new_system = pm_top_engine._system_generator.build_system(
new_topology)
pm_top_proposal = topology_proposal.TopologyProposal(
new_topology=new_topology,
new_system=new_system,
old_topology=old_topology,
old_system=old_system,
old_chemical_state_key=old_chemical_state_key,
new_chemical_state_key=new_chemical_state_key,
logp_proposal=0.0,
new_to_old_atom_map=atom_map)
assert matching_amino_found == 1
def hydrate(system, opt):
"""
This function solvates the system by using PDBFixer
Parameters:
-----------
system: OEMol molecule
The system to solvate
opt: python dictionary
The parameters used to solvate the system
Return:
-------
oe_mol: OEMol
The solvated system
"""
def BoundingBox(molecule):
"""
This function calculates the Bounding Box of the passed
molecule
molecule: OEMol
return: bb (numpy array)
the calculated bounding box is returned as numpy array:
[(xmin,ymin,zmin), (xmax,ymax,zmax)]
"""
coords = [v for k, v in molecule.GetCoords().items()]
np_coords = np.array(coords)
min_coord = np_coords.min(axis=0)
max_coord = np_coords.max(axis=0)
bb = np.array([min_coord, max_coord])
return bb
# Create a system copy
sol_system = system.CreateCopy()
# Calculate system BoundingBox (Angstrom units)
BB = BoundingBox(sol_system)
# Estimation of the box cube length in A
box_edge = 2.0 * opt['solvent_padding'] + np.max(BB[1] - BB[0])
# BB center
xc = (BB[0][0]+BB[1][0])/2.
yc = (BB[0][1]+BB[1][1])/2.
zc = (BB[0][2]+BB[1][2])/2.
delta = np.array([box_edge/2., box_edge/2., box_edge/2.]) - np.array([xc, yc, zc])
sys_coord_dic = {k: (v+delta) for k, v in sol_system.GetCoords().items()}
sol_system.SetCoords(sys_coord_dic)
# Load a fake system to initialize PDBfixer
filename = resource_filename('pdbfixer', 'tests/data/test.pdb')
fixer = PDBFixer(filename=filename)
# Convert between OE and OpenMM topology
omm_top, omm_pos = oeommutils.oemol_to_openmmTop(sol_system)
chain_names = []
for chain in omm_top.chains():
chain_names.append(chain.id)
# Set the correct topology to the fake system
fixer.topology = omm_top
fixer.positions = omm_pos
# Solvate the system
fixer.addSolvent(padding=unit.Quantity(opt['solvent_padding'], unit.angstroms),
ionicStrength=unit.Quantity(opt['salt_concentration'], unit.millimolar))
# The OpenMM topology produced by the solvation fixer has missing bond
# orders and aromaticity. The following section is creating a new openmm
# topology made of just water molecules and ions. The new topology is then
# converted in an OEMol and added to the passed molecule to produce the
# solvated system
wat_ion_top = app.Topology()
# Atom dictionary between the the PDBfixer topology and the water_ion topology
fixer_atom_to_wat_ion_atom = {}
for chain in fixer.topology.chains():
if chain.id not in chain_names:
n_chain = wat_ion_top.addChain(chain.id)
for res in chain.residues():
n_res = wat_ion_top.addResidue(res.name, n_chain)
for at in res.atoms():
n_at = wat_ion_top.addAtom(at.name, at.element, n_res)
fixer_atom_to_wat_ion_atom[at] = n_at
for bond in fixer.topology.bonds():
at0 = bond[0]
at1 = bond[1]
try:
wat_ion_top.addBond(fixer_atom_to_wat_ion_atom[at0],
fixer_atom_to_wat_ion_atom[at1], type=None, order=1)
except:
pass
wat_ion_pos = fixer.positions[len(omm_pos):]
oe_mol = oeommutils.openmmTop_to_oemol(wat_ion_top, wat_ion_pos)
# Setting the box vectors
omm_box_vectors = fixer.topology.getPeriodicBoxVectors()
box_vectors = utils.PackageOEMol.encodePyObj(omm_box_vectors)
oe_mol.SetData(oechem.OEGetTag('box_vectors'), box_vectors)
oechem.OEAddMols(oe_mol, sol_system)
return oe_mol
def __init__(self,
n_particles=1,
mass=100 * unit.amu,
Eo=3.0 * unit.kilocalories_per_mole,
a=0.5 * unit.nanometers,
b=0.5 * unit.kilocalories_per_mole,
k=1.0 * unit.kilocalories_per_mole / unit.angstroms**2,
coordinates=None):
"""Creating a new instance of DoubleWell
A new test system is returned with the openmm system of particles in an external double
well potential.
Parameters
----------
n_particles: int
Number of particles in the system
mass: unit.Quantity
Mass of the particles (in units of mass).
Eo: unit.Quantity
Parameter of the external potential with units of energy.
a: unit.Quantity
Parameter of the external potential with units of length.
b: unit.Quantity
Parameter of the external potential with units of energy.
k: unit.Quantity
Parameter of the external potential with units of energy/length^2.
Examples
--------
>>> from uibcdf_test_systems import DoubleWell
>>> from simtk import unit
>>> double_well = DoubleWell(n_particles = 1, mass = 64 * unit.amu, Eo=4.0 * unit.kilocalories_per_mole, a=1.0 * unit.nanometers, b=0.0 * unit.kilocalories_per_mole, k=1.0 * unit.kilocalories_per_mole/unit.angstroms**2))
Notes
-----
See `corresponding documentation in the user guide regarding this class
<../../systems/double_well_potential.html>`_.
"""
super().__init__()
# Parameters
self.parameters = {}
self.parameters['n_particles'] = n_particles
self.parameters['mass'] = mass
self.parameters['Eo'] = Eo
self.parameters['a'] = a
self.parameters['b'] = b
self.parameters['k'] = k
# OpenMM topology
self.topology = app.Topology()
try:
dummy_element = app.element.get_by_symbol('DUM')
except:
dummy_element = app.Element(0, 'DUM', 'DUM', 0.0 * unit.amu)
dummy_element.mass._value = mass.value_in_unit(unit.amu)
chain = self.topology.addChain('A')
for _ in range(n_particles):
residue = self.topology.addResidue('DUM', chain)
atom = self.topology.addAtom(name='DUM',
element=dummy_element,
residue=residue)
# OpenMM system
self.system = mm.System()
for _ in range(n_particles):
self.system.addParticle(dummy_element.mass)
A = Eo / (a**4)
B = -2.0 * Eo / (a**2)
C = -b / a
D = k / 2.0
force = mm.CustomExternalForce('A*x^4+B*x^2+C*x + D*(y^2+z^2)')
force.addGlobalParameter('A', A)
force.addGlobalParameter('B', B)
force.addGlobalParameter('C', C)
force.addGlobalParameter('D', D)
for ii in range(n_particles):
force.addParticle(ii, [])
_ = self.system.addForce(force)
# Coordinates
if coordinates is None:
coordinates = np.zeros([self.parameters['n_particles'], 3],
np.float32) * unit.nanometers
self.set_coordinates(coordinates)
# Potential expresion and constants
x, y, z, Eo, a, b, k = sy.symbols('x y z Eo a b k')
self.potential_expression = Eo * (
(x / a)**4 - 2.0 *
(x / a)**2) - (b / a) * x + 0.5 * k * (y**2 + z**2)
del (x, y, z, Eo, a, b, k)
def generate_topology(non_omm_topology, non_element_types=None):
if non_element_types is None:
non_element_types = set()
topology = app.Topology()
chain = topology.addChain()
if isinstance(non_omm_topology, pmd.Structure):
residue = topology.addResidue(non_omm_topology.title, chain)
atoms = dict() # pmd.Atom: omm.Atom
# Create atoms in the residue.
for pmd_atom in non_omm_topology.atoms:
name = pmd_atom.name
if pmd_atom.element in non_element_types:
element = non_element_types[pmd_atom.element]
else:
if pmd_atom.atomic_number != 0:
element = elem.Element.getByAtomicNumber(
pmd_atom.atomic_number)
else: # TODO: more robust element detection or enforcement of symbols
element = elem.Element.getBySymbol(pmd_atom.name)
omm_atom = topology.addAtom(name, element, residue)
atoms[pmd_atom] = omm_atom
omm_atom.bond_partners = []
# Create bonds.
for bond in non_omm_topology.bonds:
atom1 = atoms[bond.atom1]
atom2 = atoms[bond.atom2]
topology.addBond(atom1, atom2)
atom1.bond_partners.append(atom2)
atom2.bond_partners.append(atom1)
if non_omm_topology.box_vectors and np.any(
[x._value for x in non_omm_topology.box_vectors]):
topology.setPeriodicBoxVectors(non_omm_topology.box_vectors)
elif isinstance(non_omm_topology, mb.Compound):
residue = topology.addResidue(non_omm_topology.name, chain)
atoms = dict() # mb.Particle: omm.Atom
# Create atoms in the residue.
for mb_particle in non_omm_topology.particles():
name = mb_particle.name
if mb_particle.name in non_element_types:
element = non_element_types[mb_particle.name]
else:
element = elem.Element.getBySymbol(mb_particle.name)
omm_atom = topology.addAtom(name, element, residue)
atoms[mb_particle] = omm_atom
omm_atom.bond_partners = []
# Create bonds.
for bond in non_omm_topology.bonds():
atom1 = atoms[bond[0]]
atom2 = atoms[bond[1]]
topology.addBond(atom1, atom2)
atom1.bond_partners.append(atom2)
atom2.bond_partners.append(atom1)
bounding_box = non_omm_topology.boundingbox
box_vectors = np.zeros(shape=(3, 3))
box_vectors[0, 0] = non_omm_topology.periodicity[0] or bounding_box[0]
box_vectors[1, 1] = non_omm_topology.periodicity[1] or bounding_box[1]
box_vectors[2, 2] = non_omm_topology.periodicity[2] or bounding_box[2]
topology.setPeriodicBoxVectors(box_vectors)
else:
raise FoyerError('Unknown topology format: {}\n'
'Supported formats are: '
'"parmed.Structure", '
'"mbuild.Compound", '
'"openmm.app.Topology"'.format(topology))
return topology
def distributeLipids(boxsize,
resnames,
sigmas,
cutoff,
mass=39.9 * unit.amu, # argon
epsilon=0.238 * unit.kilocalories_per_mole, # argon,
switch_width=3.4 * unit.angstrom, # argon
):
nparticles = len(resnames)
# Determine Lennard-Jones cutoff.
cutoff = cutoff * unit.angstrom
cutoff_type = openmm.NonbondedForce.CutoffPeriodic
# Create an empty system object.
system = openmm.System()
# Periodic box vectors.
a = unit.Quantity((boxsize[0] * unit.angstrom, 0 * unit.angstrom, 0 * unit.angstrom))
b = unit.Quantity((0 * unit.angstrom, boxsize[1] * unit.angstrom, 0 * unit.angstrom))
c = unit.Quantity((0 * unit.angstrom, 0 * unit.angstrom, boxsize[2] * unit.angstrom))
system.setDefaultPeriodicBoxVectors(a, b, c)
# Set up periodic nonbonded interactions with a cutoff.
nb = openmm.NonbondedForce()
nb.setNonbondedMethod(cutoff_type)
nb.setCutoffDistance(cutoff)
nb.setUseDispersionCorrection(True)
nb.setUseSwitchingFunction(False)
if (switch_width is not None):
nb.setUseSwitchingFunction(True)
nb.setSwitchingDistance(cutoff - switch_width)
for s in sigmas:
system.addParticle(mass)
nb.addParticle(0.0 * unit.elementary_charge, s * unit.angstrom, epsilon)
positions = subrandom_particle_positions(nparticles, system.getDefaultPeriodicBoxVectors(), 2)
# Add the nonbonded force.
system.addForce(nb)
# Add a restraining potential to keep atoms in z=0
energy_expression = 'k * (z^2)'
force = openmm.CustomExternalForce(energy_expression)
force.addGlobalParameter('k', 10)
for particle_index in range(nparticles):
force.addParticle(particle_index, [])
system.addForce(force)
# Create topology.
topology = app.Topology()
chain = topology.addChain()
elems = ['Ar', 'Cl', 'Na']
_, idx = np.unique(resnames, return_inverse=True)
for i in idx:
element = app.Element.getBySymbol(elems[i])
residue = topology.addResidue(elems[i], chain)
topology.addAtom(elems[i], element, residue)
topology.setUnitCellDimensions(unit.Quantity(boxsize, unit.angstrom))
# Simulate it
from simtk.openmm import LangevinIntegrator, VerletIntegrator
from simtk.openmm.app import Simulation, PDBReporter, StateDataReporter, PDBFile
from simtk.unit import kelvin, picoseconds, picosecond, angstrom
from sys import stdout
from mdtraj.reporters import DCDReporter
nsteps = 10000
freq = 1
integrator = VerletIntegrator(0.002 * picoseconds)
simulation = Simulation(topology, system, integrator)
simulation.context.setPositions(positions)
simulation.minimizeEnergy()
# simulation.reporters.append(DCDReporter('output.dcd', 1))
# simulation.reporters.append(StateDataReporter(stdout, 1000, potentialEnergy=True, totalEnergy=True, step=True, separator=' '))
simulation.step(nsteps)
state = simulation.context.getState(getPositions=True, enforcePeriodicBox=True)
allfinalpos = state.getPositions(asNumpy=True).value_in_unit(angstrom)
# with open('topology.pdb', 'w') as f:
# PDBFile.writeFile(topology, positions, f)
# from htmd.molecule.molecule import Molecule
# mol = Molecule('topology.pdb')
# mol.read('output.dcd')
return allfinalpos
def prep_system(box_width):
# if model not in supported_models:
# raise Exception("Specified water model '%s' is not in list of supported models: %s" % (model, str(supported_models)))
# Load forcefield for solvent model and ions.
# force_fields = ['tip3p.xml']
# if ionic_strength != 0.0*unit.molar:
# force_fields.append('amber99sb.xml') # For the ions.
ff = app.ForceField('tip3p.xml')
# Create empty topology and coordinates.
top = app.Topology()
pos = unit.Quantity((), unit.angstroms)
# Create new Modeller instance.
m = app.Modeller(top, pos)
boxSize = Vec3(box_width, box_width, box_width) * unit.nanometers
# boxSize = unit.Quantity(numpy.ones([3]) * box_edge / box_edge.unit, box_edge.unit)
m.addSolvent(ff, boxSize=boxSize, model='tip3p')
system = ff.createSystem(m.getTopology(),
nonbondedMethod=app.NoCutoff,
constraints=None,
rigidWater=False)
positions = m.getPositions()
positions = unit.Quantity(np.array(positions / positions.unit),
positions.unit)
# pdb_str = io.StringIO()
fname = "debug.pdb"
fhandle = open(fname, "w")
PDBFile.writeHeader(m.getTopology(), fhandle)
PDBFile.writeModel(m.getTopology(), positions, fhandle, 0)
PDBFile.writeFooter(m.getTopology(), fhandle)
return system, positions, np.eye(3) * box_width, fname
assert 0
# , positiveIon=positive_ion,
# negativeIon=negative_ion, ionicStrength=ionic_strength)
# Get new topology and coordinates.
newtop = m.getTopology()
newpos = m.getPositions()
# Convert positions to numpy.
positions = unit.Quantity(numpy.array(newpos / newpos.unit), newpos.unit)
# Create OpenMM System.
system = ff.createSystem(newtop,
nonbondedMethod=nonbondedMethod,
nonbondedCutoff=cutoff,
constraints=None,
rigidWater=constrained,
removeCMMotion=False)
# Set switching function and dispersion correction.
forces = {
system.getForce(index).__class__.__name__: system.getForce(index)
for index in range(system.getNumForces())
}
forces['NonbondedForce'].setUseSwitchingFunction(False)
if switch_width is not None:
forces['NonbondedForce'].setUseSwitchingFunction(True)
forces['NonbondedForce'].setSwitchingDistance(cutoff - switch_width)
forces['NonbondedForce'].setUseDispersionCorrection(dispersion_correction)
forces['NonbondedForce'].setEwaldErrorTolerance(ewaldErrorTolerance)
n_atoms = system.getNumParticles()
self.ndof = 3 * n_atoms - (constrained * n_atoms)
self.topology = m.getTopology()
self.system = system
self.positions = positions
def __init__(self, nx=3, ny=3, nz=3,
K=100.0, b=2.0, mass=39.948 * unit.amu, well_radius=1.0,
grid_spacing=1.0 * unit.angstrom,
coupling_strength=100.0 * unit.kilocalories_per_mole / unit.angstrom,
**kwargs):
"""Initialize particles on a 3D grid of specified size.
Parameters
----------
nx, ny, nz : ints
number of particles in x, y, z directions, respectively
K : float
well depth
b : float
exponent
mass : simtk.unit.Quantity
particle mass
grid_spacing : simtk.unit.Quantity
increment between grid points
coupling_strength : simtk.unit.quantity
strength of HarmonicBond force between each neighboring pair of particles
Attributes
----------
topology, positions, system
"""
# 1. Initialize
# 2. Set particles on a 3D grid, use a CustomExternalForce to place each particle in a well
# 3. Add a HarmonicBondForce to each neighboring pair of particles.
### 1. Initialize
TestSystem.__init__(self, **kwargs)
# Set unit of well-depth appropriately
#K *= unit.kilocalories_per_mole / unit.angstroms ** b
# Determine total number of atoms.
natoms = nx * ny * nz
# Create an empty system object.
system = openmm.System()
### 2. Put particles on a 3D grid
positions = unit.Quantity(np.zeros([natoms, 3], np.float32), unit.angstrom)
atom_index = 0
# Store the atom indices in a 3-way array
# so that we can conveniently determine nearest neighbors
atom_indices = np.zeros((nx, ny, nz), dtype=int)
energy_expression = "{K} * (sqrt((x - x0)^2 + (y - y0)^2 + (z - z0)^2) / {r})^{b};".format(
b=b, K=K, r=well_radius)
force = openmm.CustomExternalForce(energy_expression)
force.addPerParticleParameter("x0")
force.addPerParticleParameter("y0")
force.addPerParticleParameter("z0")
for i in range(nx):
for j in range(ny):
for k in range(nz):
system.addParticle(mass)
xyz = (grid_spacing.value_in_unit(unit.angstrom)) * np.array([i, j, k], dtype=float)
positions[atom_index] = (xyz + np.random.randn(3)*0.01) * unit.angstrom
atom_indices[i, j, k] = atom_index
# Add this particle's well
force.addParticle(atom_index, xyz)
atom_index += 1
system.addForce(force)
### 3. Couple each pair of neighbors
# Find each pair of neighbors in this grid.
# Connect each particle (i,j,k), to its "forward" neighbors,
# (i+1, j, k), (i, j+1, k), (i, j, k+1),
# (if they exist)
bonds = []
for i in range(nx):
for j in range(ny):
for k in range(nz):
if (i + 1) < nx:
bonds.append((atom_indices[i, j, k], atom_indices[i + 1, j, k]))
if (j + 1) < ny:
bonds.append((atom_indices[i, j, k], atom_indices[i, j + 1, k]))
if (k + 1) < nz:
bonds.append((atom_indices[i, j, k], atom_indices[i, j, k + 1]))
# Add these HarmonicBondForces to the system
force = openmm.HarmonicBondForce()
for bond in bonds:
force.addBond(int(bond[0]), int(bond[1]), grid_spacing, coupling_strength)
system.addForce(force)
# Create topology.
topology = app.Topology()
element = app.Element.getBySymbol('Ar')
chain = topology.addChain()
for particle in range(system.getNumParticles()):
residue = topology.addResidue('Ar', chain)
topology.addAtom('Ar', element, residue)
# Set topology, positions, system as instance attributes
self.topology = topology
self.positions = positions
self.system = system
def _addAtomsToTopology(self, heavyAtomsOnly, omitUnknownMolecules):
"""Create a new Topology in which missing atoms have been added."""
newTopology = app.Topology()
newPositions = []*unit.nanometer
newAtoms = []
existingAtomMap = {}
addedAtomMap = {}
addedOXT = []
for chain in self.topology.chains():
if omitUnknownMolecules and not any(residue.name in self.templates for residue in chain.residues()):
continue
chainResidues = list(chain.residues())
newChain = newTopology.addChain()
for indexInChain, residue in enumerate(chain.residues()):
# Insert missing residues here.
if (chain.index, indexInChain) in self.missingResidues:
insertHere = self.missingResidues[(chain.index, indexInChain)]
endPosition = self._computeResidueCenter(residue)
if indexInChain > 0:
startPosition = self._computeResidueCenter(chainResidues[indexInChain-1])
else:
outward = endPosition-self.centroid
norm = unit.norm(outward)
if norm > 0*unit.nanometer:
outward *= len(insertHere)*0.5*unit.nanometer/norm
startPosition = endPosition+outward
self._addMissingResiduesToChain(newChain, insertHere, startPosition, endPosition, residue, newAtoms, newPositions)
# Create the new residue and add existing heavy atoms.
newResidue = newTopology.addResidue(residue.name, newChain)
addResiduesAfter = (residue == chainResidues[-1] and (chain.index, indexInChain+1) in self.missingResidues)
for atom in residue.atoms():
if not heavyAtomsOnly or (atom.element is not None and atom.element != hydrogen):
if atom.name == 'OXT' and (chain.index, indexInChain+1) in self.missingResidues:
continue # Remove terminal oxygen, since we'll add more residues after this one
newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
existingAtomMap[atom] = newAtom
newPositions.append(self.positions[atom.index])
if residue in self.missingAtoms:
# Find corresponding atoms in the residue and the template.
template = self.templates[residue.name]
atomPositions = dict((atom.name, self.positions[atom.index]) for atom in residue.atoms())
points1 = []
points2 = []
for atom in template.topology.atoms():
if atom.name in atomPositions:
points1.append(atomPositions[atom.name].value_in_unit(unit.nanometer))
points2.append(template.positions[atom.index].value_in_unit(unit.nanometer))
# Compute the optimal transform to overlay them.
(translate2, rotate, translate1) = _overlayPoints(points1, points2)
# Add the missing atoms.
addedAtomMap[residue] = {}
for atom in self.missingAtoms[residue]:
newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
newAtoms.append(newAtom)
addedAtomMap[residue][atom] = newAtom
templatePosition = template.positions[atom.index].value_in_unit(unit.nanometer)
newPositions.append((mm.Vec3(*np.dot(rotate, templatePosition+translate2))+translate1)*unit.nanometer)
if residue in self.missingTerminals:
terminalsToAdd = self.missingTerminals[residue]
else:
terminalsToAdd = None
# If this is the end of the chain, add any missing residues that come after it.
if residue == chainResidues[-1] and (chain.index, indexInChain+1) in self.missingResidues:
insertHere = self.missingResidues[(chain.index, indexInChain+1)]
if len(insertHere) > 0:
startPosition = self._computeResidueCenter(residue)
outward = startPosition-self.centroid
norm = unit.norm(outward)
if norm > 0*unit.nanometer:
outward *= len(insertHere)*0.5*unit.nanometer/norm
endPosition = startPosition+outward
self._addMissingResiduesToChain(newChain, insertHere, startPosition, endPosition, residue, newAtoms, newPositions)
newResidue = list(newChain.residues())[-1]
if newResidue.name in proteinResidues:
terminalsToAdd = ['OXT']
else:
terminalsToAdd = None
# If a terminal OXT is missing, add it.
if terminalsToAdd is not None:
atomPositions = dict((atom.name, newPositions[atom.index].value_in_unit(unit.nanometer)) for atom in newResidue.atoms())
if 'OXT' in terminalsToAdd:
newAtom = newTopology.addAtom('OXT', oxygen, newResidue)
newAtoms.append(newAtom)
addedOXT.append(newAtom)
d_ca_o = atomPositions['O']-atomPositions['CA']
d_ca_c = atomPositions['C']-atomPositions['CA']
d_ca_c /= unit.sqrt(unit.dot(d_ca_c, d_ca_c))
v = d_ca_o - d_ca_c*unit.dot(d_ca_c, d_ca_o)
newPositions.append((atomPositions['O']+2*v)*unit.nanometer)
newTopology.setUnitCellDimensions(self.topology.getUnitCellDimensions())
newTopology.createStandardBonds()
newTopology.createDisulfideBonds(newPositions)
# Return the results.
return (newTopology, newPositions, newAtoms, existingAtomMap)
def __init__(self,
atom_1='Ar',
atom_2='Xe',
mass_1=None,
sigma_1=None,
epsilon_1=None,
mass_2=None,
sigma_2=None,
epsilon_2=None,
cutoff_distance=None,
switching_distance=None,
box=None,
coordinates=None):
super().__init__()
# Parameters
if (mass_1 is not None) or (sigma_1 is not None) or (epsilon_1
is not None):
if mass_1 is None:
raise ValueError(
'A value for the input argument "mass_1" is needed.')
if sigma_1 is None:
raise ValueError(
'A value for the input argument "sigma_1" is needed.')
if epsilon_1 is None:
raise ValueError(
'A value for the input argument "epsilon_1" is needed.')
elif atom_1 is not None:
mass_1 = atoms_LJ[atom_1]['mass']
sigma_1 = atoms_LJ[atom_1]['sigma']
epsilon_1 = atoms_LJ[atom_1]['epsilon']
if (mass_2 is not None) or (sigma_2 is not None) or (epsilon_2
is not None):
if mass_2 is None:
raise ValueError(
'A value for the input argument "mass_2" is needed.')
if sigma_2 is None:
raise ValueError(
'A value for the input argument "sigma_2" is needed.')
if epsilon_2 is None:
raise ValueError(
'A value for the input argument "epsilon_2" is needed.')
elif atom_2 is not None:
mass_2 = atoms_LJ[atom_2]['mass']
sigma_2 = atoms_LJ[atom_2]['sigma']
epsilon_2 = atoms_LJ[atom_2]['epsilon']
self.parameters['mass_1'] = mass_1
self.parameters['sigma_1'] = sigma_1
self.parameters['epsilon_1'] = epsilon_1
self.parameters['mass_2'] = mass_2
self.parameters['sigma_2'] = sigma_2
self.parameters['epsilon_2'] = epsilon_2
if box is not None:
reduced_sigma = self.get_reduced_sigma()
if cutoff_distance is None:
cutoff_distance = 4.0 * reduced_sigma
if switching_distance is None:
switching_distance = 3.0 * reduced_sigma
self.parameters['box'] = box
self.parameters['cutoff_distance'] = cutoff_distance
self.parameters['switching_distance'] = switching_distance
# OpenMM topology
self.topology = app.Topology()
try:
dummy_element = app.element.get_by_symbol('DUM')
except:
dummy_element = app.Element(0, 'DUM', 'DUM', 0.0 * unit.amu)
chain = self.topology.addChain('A')
residue = self.topology.addResidue('DUM_0', chain)
atom = self.topology.addAtom(name='DUM_0',
element=dummy_element,
residue=residue)
residue = self.topology.addResidue('DUM_1', chain)
atom = self.topology.addAtom(name='DUM_1',
element=dummy_element,
residue=residue)
# OpenMM system
self.system = mm.System()
non_bonded_force = mm.NonbondedForce()
if box is not None:
non_bonded_force.setNonbondedMethod(
mm.NonbondedForce.CutoffPeriodic)
non_bonded_force.setUseSwitchingFunction(True)
non_bonded_force.setCutoffDistance(cutoff_distance)
non_bonded_force.setSwitchingDistance(switching_distance)
else:
non_bonded_force.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
self.system.addParticle(mass_1)
charge_1 = 0.0 * unit.elementary_charge
non_bonded_force.addParticle(charge_1, sigma_1, epsilon_1)
self.system.addParticle(mass_2)
charge_2 = 0.0 * unit.elementary_charge
non_bonded_force.addParticle(charge_2, sigma_2, epsilon_2)
_ = self.system.addForce(non_bonded_force)
# Coordinates
if coordinates is not None:
self.set_coordinates(coordinates)
# Box
if box is not None:
self.set_box(box)
# Potential expresion
d, eps_r, sigma_r = symbols('d eps_r sigma_r')
self.potential_expression = 4.0 * eps_r * ((sigma_r / d)**12 -
(sigma_r / d)**6)
del (d, eps_r, sigma_r)
def empty_topology():
"""Empty topology."""
return app.Topology()
def build_two_residues():
alanine_topology = app.Topology()
alanine_positions = unit.Quantity(np.zeros((22, 3)), unit.nanometer)
leucine_topology = app.Topology()
leucine_positions = unit.Quantity(np.zeros((31, 3)), unit.nanometer)
ala_chain = alanine_topology.addChain(id='A')
leu_chain = leucine_topology.addChain(id='A')
ala_ace = alanine_topology.addResidue('ACE', ala_chain)
ala_res = alanine_topology.addResidue('ALA', ala_chain)
ala_nme = alanine_topology.addResidue('NME', ala_chain)
leu_ace = leucine_topology.addResidue('ACE', leu_chain)
leu_res = leucine_topology.addResidue('LEU', leu_chain)
leu_nme = leucine_topology.addResidue('NME', leu_chain)
ala_atoms = dict()
leu_atoms = dict()
atom_map = dict()
for core_atom_name, [element, position] in ace.items():
position = np.asarray(position)
alanine_positions[len(ala_atoms.keys())] = position * unit.angstrom
leucine_positions[len(leu_atoms.keys())] = position * unit.angstrom
ala_atom = alanine_topology.addAtom(core_atom_name, element, ala_ace)
leu_atom = leucine_topology.addAtom(core_atom_name, element, leu_ace)
ala_atoms['ace-' + core_atom_name] = ala_atom
leu_atoms['ace-' + core_atom_name] = leu_atom
atom_map[ala_atom.index] = leu_atom.index
for core_atom_name, [element, position] in core.items():
position = np.asarray(position)
alanine_positions[len(ala_atoms.keys())] = position * unit.angstrom
leucine_positions[len(leu_atoms.keys())] = position * unit.angstrom
ala_atom = alanine_topology.addAtom(core_atom_name, element, ala_res)
leu_atom = leucine_topology.addAtom(core_atom_name, element, leu_res)
ala_atoms[core_atom_name] = ala_atom
leu_atoms[core_atom_name] = leu_atom
atom_map[ala_atom.index] = leu_atom.index
for ala_atom_name, [element, position] in ala_unique.items():
position = np.asarray(position)
alanine_positions[len(ala_atoms.keys())] = position * unit.angstrom
ala_atom = alanine_topology.addAtom(ala_atom_name, element, ala_res)
ala_atoms[ala_atom_name] = ala_atom
for leu_atom_name, [element, position] in leu_unique.items():
position = np.asarray(position)
leucine_positions[len(leu_atoms.keys())] = position * unit.angstrom
leu_atom = leucine_topology.addAtom(leu_atom_name, element, leu_res)
leu_atoms[leu_atom_name] = leu_atom
for core_atom_name, [element, position] in nme.items():
position = np.asarray(position)
alanine_positions[len(ala_atoms.keys())] = position * unit.angstrom
leucine_positions[len(leu_atoms.keys())] = position * unit.angstrom
ala_atom = alanine_topology.addAtom(core_atom_name, element, ala_nme)
leu_atom = leucine_topology.addAtom(core_atom_name, element, leu_nme)
ala_atoms['nme-' + core_atom_name] = ala_atom
leu_atoms['nme-' + core_atom_name] = leu_atom
atom_map[ala_atom.index] = leu_atom.index
for bond in core_bonds:
alanine_topology.addBond(ala_atoms[bond[0]], ala_atoms[bond[1]])
leucine_topology.addBond(leu_atoms[bond[0]], leu_atoms[bond[1]])
for bond in ala_bonds:
alanine_topology.addBond(ala_atoms[bond[0]], ala_atoms[bond[1]])
for bond in leu_bonds:
leucine_topology.addBond(leu_atoms[bond[0]], leu_atoms[bond[1]])
return alanine_topology, alanine_positions, leucine_topology, leucine_positions, atom_map
def run(opts):
system_xml_file = opts.system
integrator_xml_file = opts.integrator
coords_f = opts.coords
platform_name = opts.platform
deviceid = opts.device
write_freq = opts.write_freq
output = opts.output
nsteps = opts.nsteps
platform_properties = {
'OpenCLPrecision': 'mixed',
'OpenCLPlatformIndex': '0',
'OpenCLDeviceIndex': '0',
'CudaPrecision': 'mixed',
'CudaDeviceIndex': '0',
'CpuThreads': '1'
}
platform_properties['CudaDeviceIndex'] = deviceid
platform_properties['OpenCLDeviceIndex'] = deviceid
with open(system_xml_file, 'r') as f:
system = openmm.XmlSerializer.deserialize(f.read())
with open(integrator_xml_file, 'r') as f:
integrator = openmm.XmlSerializer.deserialize(f.read())
integrator.setRandomNumberSeed(random.randint(0, 2**16))
platform = openmm.Platform.getPlatformByName(platform_name)
properties = {
key: platform_properties[key]
for key in platform_properties
if key.lower().startswith(platform_name.lower())
}
if platform_name == 'CPU':
properties = {'CpuThreads': '1'}
print properties
# Create dummy topology to satisfy Simulation object
topology = app.Topology()
volume = wcadimer.natoms / wcadimer.density
length = volume**(1.0 / 3.0)
L = length.value_in_unit(units.nanometer)
topology.setUnitCellDimensions(Vec3(L, L, L) * units.nanometer)
simulation = app.Simulation(topology, system, integrator, platform,
properties)
init_data = np.load(coords_f)
coords = units.Quantity(init_data['coord'], units.nanometer)
simulation.context.setPositions(coords)
if 'veloc' in init_data:
velocs = units.Quantity(init_data['veloc'],
units.nanometer / units.picosecond)
simulation.context.setVelocities(velocs)
else:
simulation.context.setVelocitiesToTemperature(wcadimer.temperature)
# Attach reporters
simulation.reporters.append(
HDF5Reporter(output + '.h5', write_freq, atomSubset=[0, 1]))
simulation.reporters.append(
app.StateDataReporter(stdout,
20 * write_freq,
step=True,
potentialEnergy=True,
temperature=True,
progress=True,
remainingTime=True,
speed=True,
totalSteps=nsteps,
separator='\t'))
# Run segment
simulation.step(nsteps)
# Write restart data
state = simulation.context.getState(getPositions=True, getVelocities=True)
coords = state.getPositions(asNumpy=True)
velocs = state.getVelocities(asNumpy=True)
np.savez_compressed(output + '_restart.npz',
coords,
coord=coords,
veloc=velocs)
def extract(self, chains_to_keep, extract_protein):
'''Extract the protein or ligand from the complex and return its energy.
Parameters
----------
chains_to_keep : list of strings
Chain id(s) to keep
extract_protein : boolean
If true, extract protein. Otherwise, extract ligand.
Returns
-------
float
Final energy in kcal/mol
'''
try:
self.minimizedState.getPositions()
except Exception:
print(
"The System has not been minimized -- you must minimize before extracting."
)
if not isinstance(extract_protein, bool):
raise TypeError(
"extract_protein should be boolean indicating whether to extract the protein (True) or ligand (False)"
)
## Extract topology
if extract_protein:
print("\tExtracting P from PL...")
else:
print("\tExtracting L from PL...")
# Create new topology
new_topology = app.Topology()
# Copy residues and atoms to new topology for chains_to_keep
d_old_to_new = {
} # Key: atom in old topology, Value: atom in new topology
for chain in self.complexTopology.chains():
if chain.id in chains_to_keep:
new_chain = new_topology.addChain(id=chain.id)
for res in chain.residues():
# Copy residues and atoms
new_res = new_topology.addResidue(res.name,
new_chain,
id=res.id)
for atom in res.atoms():
new_atom = new_topology.addAtom(
atom.name, atom.element, new_res)
d_old_to_new[atom] = new_atom
# Make list of atoms to delete
atoms_to_delete = []
for res in self.complexTopology.residues():
if res.chain.id not in chains_to_keep:
for atom in res.atoms():
atoms_to_delete.append(atom)
# Copy bonds to new topology, except bonds involving atoms to delete
for bond in self.complexTopology.bonds():
atom_1 = bond[0]
atom_2 = bond[1]
if (atom_1 in atoms_to_delete) or (atom_2 in atoms_to_delete):
continue
atom_1_new = d_old_to_new[atom_1]
atom_2_new = d_old_to_new[atom_2]
new_topology.addBond(atom_1_new, atom_2_new)
## Extract the positions
atoms = [
atom.index for atom in self.complexTopology.atoms()
if atom.residue.chain.id in chains_to_keep
]
positions = [
position
for i, position in enumerate(self.minimizedState.getPositions())
if i in atoms
]
## Extract the energy
# Set up system
system = self.forcefield.createSystem(
new_topology,
nonbondedMethod=app.CutoffNonPeriodic,
nonbondedCutoff=1.2 * unit.nanometer,
constraints=app.HBonds,
hydrogenMass=4 * unit.amu,
soluteDielectric=1,
solventDielectric=1)
# Set up integrator
integrator = openmmtools.integrators.LangevinIntegrator(
300 * unit.kelvin, 1 / unit.picosecond, 4 * unit.femtosecond)
# Set up simulation
simulation = app.Simulation(new_topology, system, integrator,
self.platform)
simulation.context.setPositions(positions)
# Get the initial energy
initial_state = simulation.context.getState(getEnergy=True,
getPositions=True)
initial_energy = initial_state.getPotentialEnergy(
) / unit.kilocalories_per_mole # before conversion: kJ/mol
print('\t Energy : %8.3f kcal/mol' % (initial_energy))
if extract_protein:
self.proteinEnergy = initial_energy
else:
self.ligandEnergy = initial_energy
import pandas as pd
import simtk.openmm.app as app
import simtk.openmm as mm
import simtk.unit as u
import mdtraj as md
# 0.2 * 1000 / 18.015
temperature = 300.0 * u.kelvin
pressure = 1.0 * u.atmospheres
stderr_tolerance = 0.0001
ionicStrength = 2.0 * u.molar
ff = app.ForceField("tip3p.xml", "amber10.xml")
mmtop = app.Topology()
positions = []
modeller = app.Modeller(mmtop, positions)
modeller.addSolvent(ff,
boxSize=mm.Vec3(2.2, 2.2, 2.2) * u.nanometers,
ionicStrength=ionicStrength)
system = ff.createSystem(modeller.topology, nonbondedMethod=app.CutoffPeriodic)
output_frequency = 125
friction = 1.0 / u.picoseconds
timestep = 2.0 * u.femtoseconds
barostat_frequency = 25
n_steps = 100000
csv_filename = "density_%d_%0.1f.csv" % (temperature / temperature.unit,
import atomsmm
from simtk import openmm
from simtk import unit
from simtk.openmm import app
from sys import stdout
temp = 300 * unit.kelvin
rigid_water = False
simulation_platform = 'CUDA'
pressure_computer_platform = 'CUDA'
modeller = app.Modeller(app.Topology(), [])
force_field = app.ForceField('tip3p.xml')
modeller.addSolvent(force_field, numAdded=500)
topology = modeller.getTopology()
system = force_field.createSystem(topology,
nonbondedMethod=app.PME,
rigidWater=rigid_water)
def platform(name):
return [
openmm.Platform.getPlatformByName(name),
dict(Precision='mixed') if name == 'CUDA' else dict()
]
integrator = openmm.LangevinIntegrator(temp, 0.1 / unit.femtoseconds,
1.0 * unit.femtosecond)
system.addForce(openmm.MonteCarloBarostat(1 * unit.atmospheres, temp, 20))
simulation = app.Simulation(topology, system, integrator,
def oemol_to_openmmTop(mol):
"""
This function converts an OEMol to an openmm topology
The OEMol coordinates are assumed to be in Angstrom unit
Parameters:
-----------
mol: OEMol molecule
The molecule to convert
Return:
-------
topology : OpenMM Topology
The generated OpenMM topology
positions : OpenMM Quantity
The molecule atom positions associated with the
generated topology in Angstrom units
"""
# OE Hierarchical molecule view
hv = oechem.OEHierView(
mol, oechem.OEAssumption_BondedResidue +
oechem.OEAssumption_ResPerceived + oechem.OEAssumption_PDBOrder)
# Create empty OpenMM Topology
topology = app.Topology()
# Dictionary used to map oe atoms to openmm atoms
oe_atom_to_openmm_at = {}
for chain in hv.GetChains():
# Create empty OpenMM Chain
openmm_chain = topology.addChain(chain.GetChainID())
for frag in chain.GetFragments():
for hres in frag.GetResidues():
# Get OE residue
oe_res = hres.GetOEResidue()
# Create OpenMM residue
openmm_res = topology.addResidue(oe_res.GetName(),
openmm_chain)
for oe_at in hres.GetAtoms():
# Select atom element based on the atomic number
element = app.element.Element.getByAtomicNumber(
oe_at.GetAtomicNum())
# Add atom OpenMM atom to the topology
openmm_at = topology.addAtom(oe_at.GetName(), element,
openmm_res)
openmm_at.index = oe_at.GetIdx()
# Add atom to the mapping dictionary
oe_atom_to_openmm_at[oe_at] = openmm_at
if topology.getNumAtoms() != mol.NumAtoms():
raise ValueError(
"OpenMM topology and OEMol number of atoms mismatching: "
"OpenMM = {} vs OEMol = {}".format(topology.getNumAtoms(),
mol.NumAtoms()))
# Count the number of bonds in the openmm topology
omm_bond_count = 0
def IsAmideBond(oe_bond):
# This supporting function checks if the passed bond is an amide bond or not.
# Our definition of amide bond C-N between a Carbon and a Nitrogen atom is:
# O
# ║
# CA or O-C-N-
# |
# The amide bond C-N is a single bond
if oe_bond.GetOrder() != 1:
return False
atomB = oe_bond.GetBgn()
atomE = oe_bond.GetEnd()
# The amide bond is made by Carbon and Nitrogen atoms
if not (atomB.IsCarbon() and atomE.IsNitrogen() or
(atomB.IsNitrogen() and atomE.IsCarbon())):
return False
# Select Carbon and Nitrogen atoms
if atomB.IsCarbon():
C_atom = atomB
N_atom = atomE
else:
C_atom = atomE
N_atom = atomB
# Carbon and Nitrogen atoms must have 3 neighbour atoms
if not (C_atom.GetDegree() == 3 and N_atom.GetDegree() == 3):
return False
double_bonds = 0
single_bonds = 0
for bond in C_atom.GetBonds():
# The C-O bond can be single or double.
if (bond.GetBgn() == C_atom and bond.GetEnd().IsOxygen()) or \
(bond.GetBgn().IsOxygen() and bond.GetEnd() == C_atom):
if bond.GetOrder() == 2:
double_bonds += 1
if bond.GetOrder() == 1:
single_bonds += 1
# The CA-C bond is single
if (bond.GetBgn() == C_atom and bond.GetEnd().IsCarbon()) or \
(bond.GetBgn().IsCarbon() and bond.GetEnd() == C_atom):
if bond.GetOrder() == 1:
single_bonds += 1
# Just one double and one single bonds are connected to C
# In this case the bond is an amide bond
if double_bonds == 1 and single_bonds == 1:
return True
else:
return False
# Creating bonds
for oe_bond in mol.GetBonds():
omm_bond_count += 1
# Set the bond type
if oe_bond.GetType() is not "":
if oe_bond.GetType() in [
'Single', 'Double', 'Triple', 'Aromatic', 'Amide'
]:
omm_bond_type = oe_bond.GetType()
else:
omm_bond_type = None
else:
if oe_bond.IsAromatic():
oe_bond.SetType("Aromatic")
omm_bond_type = "Aromatic"
elif oe_bond.GetOrder() == 2:
oe_bond.SetType("Double")
omm_bond_type = "Double"
elif oe_bond.GetOrder() == 3:
oe_bond.SetType("Triple")
omm_bond_type = "Triple"
elif IsAmideBond(oe_bond):
oe_bond.SetType("Amide")
omm_bond_type = "Amide"
elif oe_bond.GetOrder() == 1:
oe_bond.SetType("Single")
omm_bond_type = "Single"
else:
omm_bond_type = None
topology.addBond(oe_atom_to_openmm_at[oe_bond.GetBgn()],
oe_atom_to_openmm_at[oe_bond.GetEnd()],
type=omm_bond_type,
order=oe_bond.GetOrder())
if omm_bond_count != mol.NumBonds():
raise ValueError(
"OpenMM topology and OEMol number of bonds mismatching: "
"OpenMM = {} vs OEMol = {}".format(omm_bond_count,
mol.NumBonds()))
dic = mol.GetCoords()
positions = [Vec3(v[0], v[1], v[2])
for k, v in dic.items()] * unit.angstrom
return topology, positions
def __init__(self,
box_edge=25.0 * unit.angstroms,
cutoff=9 * unit.angstroms,
model='tip3p',
switch_width=1.5 * unit.angstroms,
constrained=True,
dispersion_correction=True,
nonbondedMethod=app.PME,
ewaldErrorTolerance=5E-4,
**kwargs):
"""
Create a water box test system.
Parameters
----------
box_edge : simtk.unit.Quantity with units compatible with nanometers, optional, default = 2.5 nm
Edge length for cubic box [should be greater than 2*cutoff]
cutoff : simtk.unit.Quantity with units compatible with nanometers, optional, default = 0.9 nm
Nonbonded cutoff
model : str, optional, default = 'tip3p'
The name of the water model to use ['tip3p', 'tip4p', 'tip4pew', 'tip5p', 'spce']
switch_width : simtk.unit.Quantity with units compatible with nanometers, optional, default = 0.5 A
Sets the width of the switch function for Lennard-Jones.
constrained : bool, optional, default=True
Sets whether water geometry should be constrained (rigid water implemented via SETTLE) or flexible.
dispersion_correction : bool, optional, default=True
Sets whether the long-range dispersion correction should be used.
nonbondedMethod : simtk.openmm.app nonbonded method, optional, default=app.PME
Sets the nonbonded method to use for the water box (one of app.CutoffPeriodic, app.Ewald, app.PME).
ewaldErrorTolerance : float, optional, default=5E-4
The Ewald or PME tolerance. Used only if nonbondedMethod is Ewald or PME.
Examples
--------
Create a default waterbox.
>>> waterbox = WaterBox()
>>> [system, positions] = [waterbox.system, waterbox.positions]
Use reaction-field electrostatics instead.
>>> waterbox = WaterBox(nonbondedMethod=app.CutoffPeriodic)
Control the cutoff.
>>> waterbox = WaterBox(box_edge=3.0*unit.nanometers, cutoff=1.0*unit.nanometers)
Use a different water model.
>>> waterbox = WaterBox(model='spce')
Use a five-site water model.
>>> waterbox = WaterBox(model='tip5p')
Turn off the switch function.
>>> waterbox = WaterBox(switch_width=None)
Set the switch width.
>>> waterbox = WaterBox(switch_width=0.8*unit.angstroms)
Turn of long-range dispersion correction.
>>> waterbox = WaterBox(dispersion_correction=False)
"""
TestSystem.__init__(self, **kwargs)
supported_models = ['tip3p', 'tip4pew', 'tip5p', 'spce']
if model not in supported_models:
raise Exception(
"Specified water model '%s' is not in list of supported models: %s"
% (model, str(supported_models)))
# Load forcefield for solvent model.
ff = app.ForceField('gcmc.xml')
# Create empty topology and coordinates.
top = app.Topology()
pos = unit.Quantity((), unit.angstroms)
# Create new Modeller instance.
m = app.Modeller(top, pos)
# Add solvent to specified box dimensions.
boxSize = unit.Quantity(
np.ones([3]) * box_edge / box_edge.unit, box_edge.unit)
m.addSolvent(ff,
boxSize=boxSize,
model=model,
neutralize=False,
positiveIon='Na+',
negativeIon='Cl-',
**kwargs)
# Get new topology and coordinates.
newtop = m.getTopology()
newpos = m.getPositions()
# Convert positions to np.
positions = unit.Quantity(np.array(newpos / newpos.unit), newpos.unit)
# Create OpenMM System.
self.forcefieldOptions = {
'nonbondedMethod': nonbondedMethod,
'nonbondedCutoff': cutoff,
'constraints': None,
'rigidWater': constrained,
'removeCMMotion': False
}
system = ff.createSystem(newtop, **(self.forcefieldOptions))
# Set switching function and dispersion correction.
forces = {
system.getForce(index).__class__.__name__: system.getForce(index)
for index in range(system.getNumForces())
}
forces['NonbondedForce'].setUseSwitchingFunction(False)
if switch_width is not None:
forces['NonbondedForce'].setUseSwitchingFunction(True)
forces['NonbondedForce'].setSwitchingDistance(cutoff -
switch_width)
forces['NonbondedForce'].setUseDispersionCorrection(
dispersion_correction)
forces['NonbondedForce'].setEwaldErrorTolerance(ewaldErrorTolerance)
self.ndof = 3 * system.getNumParticles() - 3 * constrained
self.topology = newtop
self.system = system
self.positions = positions
self.forcefield = ff
import numpy as np
import argparse
import subprocess
# Read filename
parser = argparse.ArgumentParser(description='correct equilibrated.pdb')
parser.add_argument('name', type=str, help='name of file for which to correct')
args = parser.parse_args()
pdb = app.PDBFile(args.name)
# Get old topology and positions
old_topology = pdb.getTopology()
old_positions = pdb.positions
# Create new topology and positions
new_topology = app.Topology()
new_topology.setPeriodicBoxVectors(old_topology.getPeriodicBoxVectors())
positions_R, positions_X, positions_C, positions_D, positions_E, positions_Y = list(
), list(), list(), list(), list(), list()
# Create new chains
new_chain_R = new_topology.addChain(id="R")
new_chain_X = new_topology.addChain(id="X")
new_chain_C = new_topology.addChain(id="C")
new_chain_D = new_topology.addChain(id="D")
new_chain_E = new_topology.addChain(id="E")
new_chain_Y = new_topology.addChain(id="Y")
# Specify the starting residue ids for each chain
d_current_start = {"C": 18, "E": 1, "R": 332, "X": 1, "D": 1}