Example of a use case that requires Interchange.from_openmm

[j-wags]

Description

This example would set up and run a brief simulation of a small nucleic acid with a large surfactant molecule (too large for AM1BCC, must use NAGL)

• Start with
  • pre-packed PDB with NA, surfactants, waters, and ions
  • Surfactant SDF or SMILES
• Split surfactants, waters, and ions into PDB A and NA into PDB B
• Load PDB A using Topology.from_pdb(unique_molecules=[surfactant]), assign surfactant charges using NAGL (0.3.0), make an Interchange using sage-2.1.0 and charge_from_molecules
• Load PDB B using OpenMM, apply an AMBER NA and water+ions FF to it, run Interchange.from_openmm
• final_interchange = interchange_from_pdb_A + interchange_from_pdb_B