{"action":"opened","number":164,"pull_request":{"url":"https://api.github.com/repos/choderalab/openmoltools/pulls/164","id":55589040,"html_url":"https://github.com/choderalab/openmoltools/pull/164","diff_url":"https://github.com/choderalab/openmoltools/pull/164.diff","patch_url":"https://github.com/choderalab/openmoltools/pull/164.patch","issue_url":"https://api.github.com/repos/choderalab/openmoltools/issues/164","number":164,"state":"open","locked":false,"title":"[WIP] Implement GAFF/AM1-BCC residue template generator for simtk.openmm.app.ForceField","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"body":"This is the beginning of the implementation of a GAFF/AM1-BCC residue template generator for small molecules for use with the new `simtk.openmm.app.ForceField` ability to hook in residue template generators.\r\n\r\nExample usage:\r\n```python\r\nfrom simtk.openmm.app import ForceField, NoCutoff\r\n# Load my PDB file containing a ligand\r\npdb = PDBFile(pdb_filename)\r\n# Create a ForceField object, loading GAFF parameters.\r\nforcefield = ForceField('amber99sbildn.xml', 'tip3p.xml', 'gaff.xml')\r\n# Register the GAFF residue template generator.\r\nfrom openmoltools.forcefield_generators import gaffTemplateGenerator\r\nforcefield.registerTemplateGenerator(gaffTemplateGenerator)\r\n# Create an OpenMM system, calling antechamber as needed to parameterize small molecules.\r\nsystem = forcefield.createSystem(pdb.topology, nonbondedMethod=NoCutoff)\r\n```\r\n\r\nNote that this does not yet work with residues that have external bonds (like unnatural amino acids or covalently-attached ligands), but that feature is coming soon.\r\n\r\nThere are several hurdles to be overcome:\r\n- [ ] Test and debug bond order perception\r\n- [ ] Extra parameters generated by `parmchk2` need to be incorporated\r\n- [ ] Find a solution for molecules for multiple chiral 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