You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
{{ message }}
Repository navigation
Error: NoneType object has no attribute "used" #1423
Hello,
I ran a simulation for a short peptide with OpenMM 8.2.0 using the following code:
modeller = app.Modeller(pdb_object.topology, pdb_object.positions)
force_field = openmm.app.ForceField(*force_fields)
modeller.addHydrogens(forcefield=force_field, pH=7)
modeller.addSolvent(force_field,
padding = boxPadding*unit.nanometer,
boxShape = "cube",
ionicStrength = 0.15*unit.molar)
system = force_field.createSystem(modeller.topology,
nonbondedMethod = PME,
nonbondedCutoff = 1.2*ou.nanometer,
constraints = HBonds)
restraint = openmm.CustomExternalForce('k*periodicdistance(x, y, z, x0, y0, z0)^2')
system.addForce(restraint)
restraint.addGlobalParameter('k', restraint_const*openmm.unit.kilojoules_per_mole/openmm.unit.nanometer**2)
restraint.addPerParticleParameter('x0')
restraint.addPerParticleParameter('y0')
restraint.addPerParticleParameter('z0')
...
topology_file = parmed.openmm.load_topology(modeller.topology, system)
for ff in force_fields:
if "amber" in ff:
topology_file.save(f"{output_dir}/topology.prmtop")
if "charmm" in ff:
topology_file.save(f"{output_dir}/topology.psf")
I then encountered this error: NoneType object has no attribute "used". It was unclear which object returned this error.
I then took a look at the topology_file.bonds.type. Every bond return type = None.
I am relatively new to ParmED. Please help me troubleshoot this error.
I have uploaded the file related to the pdb_object here.
Thank you,
Hoa
Activity