get_subtopology function missing when parameterize openmm system #39
Description
NameError Traceback (most recent call last)
Cell In[12], line 9
5 grappa_ff = OpenmmGrappa.from_tag('grappa-1.4.1-radical')
7 # Overwrite bonded parameters with those predicted by grappa.
8 # Grappa will neither change the ion or solvent nor the nonbonded parameters.
----> 9 system_1 = grappa_ff.parametrize_system(system_1, pdb.topology, plot_dir='.')
File ~/anaconda3/envs/grappa/lib/python3.10/site-packages/grappa/wrappers/openmm_wrapper.py:60, in OpenmmGrappa.parametrize_system(self, system, topology, exclude_residues, plot_dir, charge_model)
54 warnings.warn("The charge_model argument for OpenmmGrappa.parametrize_system is deprecated, has no effect and will be removed in the future.", DeprecationWarning)
56 # convert openmm_topology (and system due to partial charges and impropers) to a Molecule
57
58 # create a sub topology excluding certain residue names (e.g. water, ions)
59 # the atom.id of the atoms in this sub topology will be the same as the atom index in the original topology, i.e. as in the system.
---> 60 sub_topology = get_subtopology(topology, exclude_residues=exclude_residues)
62 molecule = Molecule.from_openmm_system(openmm_system=system, openmm_topology=sub_topology)
64 try:
NameError: name 'get_subtopology' is not defined