T019: ValueError: No template found for residue 444 (03P)

[dominiquesydow]

T019 runs into the following error (seen in CI and locally):

____ teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 14 ____
[gw0] darwin -- Python 3.8.15 /usr/local/miniconda/envs/teachopencadd/bin/python
Notebook cell execution failed
Cell 14: Cell outputs differ

Input:
complex_topology, complex_positions = merge_protein_and_ligand(prepared_protein, omm_ligand)
print("Complex topology has", complex_topology.getNumAtoms(), "atoms.")
# NBVAL_CHECK_OUTPUT

Traceback:
Unexpected output fields from running code: {'stderr'}

____ teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 17 ____
[gw0] darwin -- Python 3.8.15 /usr/local/miniconda/envs/teachopencadd/bin/python
Notebook cell execution failed
Cell 17: Cell execution caused an exception

Input:
modeller = app.Modeller(complex_topology, complex_positions)
modeller.addSolvent(forcefield, padding=1.0 * unit.nanometers, ionicStrength=0.15 * unit.molar)

Traceback:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[18], line 2
      1 modeller = app.Modeller(complex_topology, complex_positions)
----> 2 modeller.addSolvent(forcefield,padding=1.0*unit.nanometers,ionicStrength=0.15*unit.molar)

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/openmm/app/modeller.py:483, in Modeller.addSolvent(self, forcefield, model, boxSize, boxVectors, padding, numAdded, positiveIon, negativeIon, ionicStrength, neutralize)
    479         raise ValueError('Neither the box size, box vectors, nor padding was specified, and the Topology does not define unit cell dimensions')
    481 # Have the ForceField build a System for the solute from which we can determine van der Waals radii.
--> 483 system = forcefield.createSystem(self.topology)
    484 nonbonded = None
    485 for i in range(system.getNumForces()):

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/openmm/app/forcefield.py:1212, in ForceField.createSystem(self, topology, nonbondedMethod, nonbondedCutoff, constraints, rigidWater, removeCMMotion, hydrogenMass, residueTemplates, ignoreExternalBonds, switchDistance, flexibleConstraints, drudeMass, **args)
   1208 rigidResidue = [False]*topology.getNumResidues()
   1210 # Find the template matching each residue and assign atom types.
-> 1212 templateForResidue = self._matchAllResiduesToTemplates(data,topology,residueTemplates,ignoreExternalBonds)
   1213 for res in topology.residues():
   1214     if res.name == 'HOH':
   1215         # Determine whether this should be a rigid water.

File /usr/local/miniconda/envs/teachopencadd/lib/python3.8/site-packages/openmm/app/forcefield.py:1[42](https://github.com/volkamerlab/teachopencadd/actions/runs/3796013276/jobs/6455699818#step:8:43)7, in ForceField._matchAllResiduesToTemplates(self, data, topology, residueTemplates, ignoreExternalBonds, ignoreExtraParticles, recordParameters)
   1425                 break
   1426 if matches is None:
-> 1427     raise ValueError('No template found for residue %d (%s).  %s' % (res.index+1, res.name, _findMatchErrors(self, res)))
   1428 else:
   1429     if recordParameters:

ValueError: No template found for residue 444 (03P).  This might mean your input topology is missing some atoms or bonds, or possibly that you are using the wrong force field.
`
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[dominiquesydow]

Hi @AndreaVolkamer, is there anyone in your group who could take a look at this issue?

[mbackenkoehler]

Solved by #308