---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[8], line 1
----> 1 molsys_cub = msm.build.solvate(molsys, box_shape='cubic', clearance='14.0 angstroms')
2 molsys_oct = msm.build.solvate(molsys, box_shape='truncated octahedral', clearance='14.0 angstroms')
3 molsys_dod = msm.build.solvate(molsys, box_shape='rhombic dodecahedral', clearance='14.0 angstroms')
File ~/repos@uibcdf/molsysmt/molsysmt/_private/digestion/digest.py:122, in digest.<locals>.digestor.<locals>.wrapper(*args, **kwargs)
120 return func(all_args['self'], **final_args)
121 else:
--> 122 return func(**final_args)
File ~/repos@uibcdf/molsysmt/molsysmt/build/solvate.py:115, in solvate(molecular_system, box_shape, clearance, anion, n_anions, cation, n_cations, ionic_strength, water_model, engine, to_form, verbose)
110 modeller.addSolvent(openmm_forcefield, model=solvent_model, boxVectors = box_vectors, ionicStrength=ionic_strength,
111 positiveIon=cation, negativeIon=anion)
113 else:
--> 115 modeller.addSolvent(openmm_forcefield, model=solvent_model, padding=clearance,
116 ionicStrength=ionic_strength, positiveIon=cation,
117 negativeIon=anion)
119 # fixing a bug of OpenMM
120 list_atoms = list(modeller.topology.atoms())
File ~/Myopt/miniconda3/envs/molsysmt@uibcdf_3.12/lib/python3.12/site-packages/openmm/app/modeller.py:521, in Modeller.addSolvent(self, forcefield, model, boxSize, boxVectors, padding, numAdded, boxShape, positiveIon, negativeIon, ionicStrength, neutralize, residueTemplates)
517 raise ValueError('Neither the box size, box vectors, nor padding was specified, and the Topology does not define unit cell dimensions')
519 # Have the ForceField build a System for the solute from which we can determine van der Waals radii.
--> 521 system = forcefield.createSystem(self.topology, residueTemplates=residueTemplates)
522 nonbonded = None
523 for i in range(system.getNumForces()):
File ~/Myopt/miniconda3/envs/molsysmt@uibcdf_3.12/lib/python3.12/site-packages/openmm/app/forcefield.py:1266, in ForceField.createSystem(self, topology, nonbondedMethod, nonbondedCutoff, constraints, rigidWater, removeCMMotion, hydrogenMass, residueTemplates, ignoreExternalBonds, switchDistance, flexibleConstraints, drudeMass, **args)
1262 rigidResidue = [False]*topology.getNumResidues()
1264 # Find the template matching each residue and assign atom types.
-> 1266 templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
1267 for res in topology.residues():
1268 if res.name == 'HOH':
1269 # Determine whether this should be a rigid water.
File ~/Myopt/miniconda3/envs/molsysmt@uibcdf_3.12/lib/python3.12/site-packages/openmm/app/forcefield.py:1486, in ForceField._matchAllResiduesToTemplates(self, data, topology, residueTemplates, ignoreExternalBonds, ignoreExtraParticles, recordParameters)
1484 break
1485 if matches is None:
-> 1486 raise ValueError('No template found for residue %d (%s). %s For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template' % (res.index, res.name, _findMatchErrors(self, res)))
1487 else:
1488 if recordParameters:
ValueError: No template found for residue 0 (TYR). The atoms and bonds in the residue match TYR, but the set of externally bonded atoms is missing 1 N atom. Is the chain missing a terminal capping group? For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template
