{"action":"created","comment":{"url":"https://api.github.com/repos/choderalab/yank/pulls/comments/93952451","pull_request_review_id":14483379,"id":93952451,"diff_hunk":"@@ -338,6 +339,12 @@ def prepare_phase(positions_file_path, parameters_file_path, ligand_dsl, system_\n             logger.info(\"gro: %s\" % positions_file_path)\n \n         positions_file = openmm.app.GromacsGroFile(positions_file_path)\n+        if ('nonbonded_method' in system_options) and (system_options['nonbonded_method'] in _NONPERIODIC_NONBONDED_METHODS):","path":"Yank/pipeline.py","position":36,"original_position":36,"commit_id":"5be11a39e78da530c2406be443ae1539f7d69e1b","original_commit_id":"5be11a39e78da530c2406be443ae1539f7d69e1b","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":"The second part of the conditional is only evaluated if the first part evaluates to `True`.","created_at":"2016-12-27T17:21:17Z","updated_at":"2016-12-27T17:21:17Z","html_url":"https://github.com/choderalab/yank/pull/614#discussion_r93952451","pull_request_url":"https://api.github.com/repos/choderalab/yank/pulls/614","_links":{"self":{"href":"https://api.github.com/repos/choderalab/yank/pulls/comments/93952451"},"html":{"href":"https://github.com/choderalab/yank/pull/614#discussion_r93952451"},"pull_request":{"href":"https://api.github.com/repos/choderalab/yank/pulls/614"}}},"pull_request":{"url":"https://api.github.com/repos/choderalab/yank/pulls/614","id":99274738,"html_url":"https://github.com/choderalab/yank/pull/614","diff_url":"https://github.com/choderalab/yank/pull/614.diff","patch_url":"https://github.com/choderalab/yank/pull/614.patch","issue_url":"https://api.github.com/repos/choderalab/yank/issues/614","number":614,"state":"open","locked":false,"title":"Fix #613: gromacs input file support for transfer free energies","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":"Fixes #613\r\n\r\nSo far, I've just added more debug information, but the failure is puzzling:\r\n```\r\n[LSKI1497:yank-examples/examples/gromacs] choderaj% yank script --yaml gaff.yaml\r\n2016-12-23 14:21:09,182: MPI disabled.\r\n2016-12-23 14:21:09,185: ERROR - yank.yamlbuild - System smarty-system: _system_files(['methanol_cyclohexane_1_300.gro', 'methanol_cyclohexane_1_300.top']) raised RuntimeError(\"Wrong system file types provided.\\nExtensions provided: ['gro', 'top']\\nExpected extensions: ['pdb', 'xml']\\n\",)\r\nTraceback (most recent call last):\r\n  File \"/Users/choderaj/miniconda/bin//yank\", line 9, in <module>\r\n    load_entry_point('yank==0.15.0.dev0', 'console_scripts', 'yank')()\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/yank/cli.py\", line 74, in main\r\n    dispatched = getattr(commands, command).dispatch(command_args)\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/yank/commands/script.py\", line 58, in dispatch\r\n    yaml_builder = YamlBuilder(yaml_source=yaml_path)\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/yank/yamlbuild.py\", line 1208, in __init__\r\n    self.parse(yaml_source)\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/yank/yamlbuild.py\", line 1279, in parse\r\n    self._db.systems = self._validate_systems(yaml_content.get('systems', {}))\r\n  File \"/Users/choderaj/miniconda/lib/python2.7/site-packages/yank/yamlbuild.py\", line 1819, in _validate_systems\r\n    raise YamlParseError('System {}: {}'.format(system_id, e.autos[-1]))\r\nyank.yamlbuild.YamlParseError: System smarty-system: _system_files(['methanol_cyclohexane_1_300.gro', 'methanol_cyclohexane_1_300.top']) raised RuntimeError(\"Wrong system file types provided.\\nExtensions provided: ['gro', 'top']\\nExpected extensions: ['pdb', 'xml']\\n\",)\r\n```\r\nI suspect what is happening is that the logic tries to run through every available schema to see if one works, and if none of them work, only the *final* failure error message is 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