def __init__(self, pdb, k=1000*kilojoules_per_mole/nanometer**2):
self.atom1, self.atom2, self._r0 = self.end_to_end_CA_distance(
pdb.topology, pdb.getPositions(asNumpy=True))
self.k = k.in_units_of(kilojoules_per_mole/nanometer**2)
self.force = CustomBondForce("0.5*pullingforce_k*(r-pullingforce_r0)^2")
self.force.addGlobalParameter('pullingforce_k', self.k)
self.force.addGlobalParameter('pullingforce_r0', self._r0)
self.force.addBond(self.atom1, self.atom2, [])
class PullingForceWrapper(object):
def __init__(self, pdb, k=1000*kilojoules_per_mole/nanometer**2):
self.atom1, self.atom2, self._r0 = self.end_to_end_CA_distance(
pdb.topology, pdb.getPositions(asNumpy=True))
self.k = k.in_units_of(kilojoules_per_mole/nanometer**2)
self.force = CustomBondForce("0.5*pullingforce_k*(r-pullingforce_r0)^2")
self.force.addGlobalParameter('pullingforce_k', self.k)
self.force.addGlobalParameter('pullingforce_r0', self._r0)
self.force.addBond(self.atom1, self.atom2, [])
def end_to_end_CA_distance(self, topology, positions):
residues = list(topology.residues())
# get the index of the first and last alpha carbons
i1 = [a.index for a in residues[0].atoms() if a.name == 'CA'][0]
i2 = [a.index for a in residues[-1].atoms() if a.name == 'CA'][0]
# get the current distanc be between the two alpha carbons
return i1, i2, sqrt(sum((positions[i1] - positions[i2])**2))
def get_r0(self):
return self._r0
def set_r0(self, value, context):
value = value.in_units_of(nanometer)
self._r0 = value
context.setParameter('pullingforce_r0', value)
def add_to_system(self, system):
system.addForce(self.force)
# Load the AMBER files
print("Creating OpenMM system from AMBER input files...")
prmtop = AmberPrmtopFile(amber_prmtop_file)
inpcrd = AmberInpcrdFile(amber_inpcrd_file)
system = prmtop.createSystem(
nonbondedMethod=nonbonded_method,
constraints=constraints,
temperature=temperature,
removeCMMotion=remove_cm_motion,
hydrogenMass=hydrogen_mass,
)
# Add virtual bond between RBD (CA of VAL172 ) and ACE2 (CA of GLN514)
force = CustomBondForce('0')
force.addBond(2636, 8116, [])
system.addForce(force)
# Add a barostat to the system
system.addForce(MonteCarloBarostat(pressure, temperature))
# Make and serialize integrator - Langevin dynamics
print("Serializing integrator to %s" % integrator_xml_filename)
integrator = openmmtools.integrators.LangevinIntegrator(
temperature,
collision_rate, # Friction coefficient
timestep,
constraint_tolerance=1e-5)
with open(output_prefix + integrator_xml_filename, "w") as outfile:
xml = mm.XmlSerializer.serialize(integrator)
