{"action":"closed","issue":{"url":"https://api.github.com/repos/pandegroup/pdbfixer/issues/101","labels_url":"https://api.github.com/repos/pandegroup/pdbfixer/issues/101/labels{/name}","comments_url":"https://api.github.com/repos/pandegroup/pdbfixer/issues/101/comments","events_url":"https://api.github.com/repos/pandegroup/pdbfixer/issues/101/events","html_url":"https://github.com/pandegroup/pdbfixer/issues/101","id":98287790,"number":101,"title":"Testing that bonds for mutated residues are correct","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},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-07-30T23:47:32Z","updated_at":"2015-08-01T04:06:51Z","closed_at":"2015-08-01T04:06:51Z","body":"I have an unusual issue in which I use the output of `PDBFixer` as input into `simtk.openmm.app.Modeller` and `ForceField` via\r\n```\r\nfixer.applyMutations(mutant, chain_id_to_mutate)  \r\nfixer.findMissingResidues()                                                                                                                                                                                                                                                       \r\nfixer.findMissingAtoms()                                                                                                                                                                                                                                                          \r\nfixer.addMissingAtoms()                                                                                                                                                                                                                                                           \r\nfixer.removeHeterogens(keepWater=keep_crystallographic_water)                                                                                                                                                                                                                     fixer.addMissingHydrogens(pH)  \r\n...\r\nforcefield = app.ForceField(ff_name+'.xml', water_name+'.xml')                                                                                                                                                                                                                    \r\nmodeller = app.Modeller(fixer.topology, fixer.positions)\r\nsystem = forcefield.createSystem(modeller.topology, nonbondedMethod=nonbonded_method, nonbondedCutoff=nonbonded_cutoff, constraints=app.HBonds)\r\n```\r\nand run into this error:\r\n```\r\nTraceback (most recent call last):\r\n  File \"setup_mutations_ensembler.py\", line 210, in <module>\r\n    system = forcefield.createSystem(modeller.topology, nonbondedMethod=nonbonded_method, nonbondedCutoff=nonbonded_cutoff, constraints=app.HBonds)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/simtk/openmm/app/forcefield.py\", line 380, in createSystem\r\n    raise ValueError('No template found for residue %d (%s).  %s' % (res.index+1, res.name, _findMatchErrors(self, res)))\r\nValueError: No template found for residue 324 (PRO).  The set of atoms matches PRO, but the bonds are different.\r\n```\r\nI suspect that this is because the atom names end up correct, but `fixer.topology` has some incorrect bonds.  This is not a terminal residue.\r\n\r\nIf I added some extra unit tests to make sure that a mutation to PRO has the expected bond pattern, what would the best way to do that be?\r\n\r\nIn the meantime, I will simply reload the PDB file to get around this."}}