When generating a new forcefield from a smiles string using ff_generation.ipynb the resulting mol2 and forcefield do not polymerize. Polymerization works exactly as intended, but when running the code below the following error occurs. Additionally the monomer does not error out when running a hoomd simulation. The full error can be found in the attached .txt file
espmol = espaloma_mol(system_file)
molecule = Molecule(num_mols=1, compound=espmol)
molff = FF_from_file(ff_filepath)
system = Pack(molecules=molecule,density=0.01 * u.g/u.cm**3,packing_expand_factor=5)
system.apply_forcefield(r_cut=2.5, force_field=molff, auto_scale=True,remove_charges=True, remove_hydrogens=True)
ParameterizationError: No parameters found for connection <Dihedral Dihedral, id: 139782542540176>,
group: dihedral_type, identifiers: [['N2', 'C0', 'C0', 'S1'], ['N2', 'C0', 'C0', 'S1']] in the Forcefield.
ParameterizationError.txt
When generating a new forcefield from a smiles string using ff_generation.ipynb the resulting mol2 and forcefield do not polymerize. Polymerization works exactly as intended, but when running the code below the following error occurs. Additionally the monomer does not error out when running a hoomd simulation. The full error can be found in the attached .txt file
ParameterizationError.txt