{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/yank/issues/261","labels_url":"https://api.github.com/repos/choderalab/yank/issues/261/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/yank/issues/261/comments","events_url":"https://api.github.com/repos/choderalab/yank/issues/261/events","html_url":"https://github.com/choderalab/yank/pull/261","id":88914869,"number":261,"title":"[WIP] Added draft of MHC-peptide-TCR setup using Yank Python API","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":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-06-17T05:22:17Z","updated_at":"2015-06-20T20:49:23Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/choderalab/yank/pulls/261","html_url":"https://github.com/choderalab/yank/pull/261","diff_url":"https://github.com/choderalab/yank/pull/261.diff","patch_url":"https://github.com/choderalab/yank/pull/261.patch"},"body":"I've used `pdbfixer`, `mdtraj`, and the Yank Python API to set up a MHC-peptide-TCR free energy calculation.\r\n\r\nWhile the `Yank` API is simple, there's a fair amount of work that needs to be done to get to this point, so we should think about what we can do to help make this easier."},"comment":{"url":"https://api.github.com/repos/choderalab/yank/issues/comments/113818800","html_url":"https://github.com/choderalab/yank/pull/261#issuecomment-113818800","issue_url":"https://api.github.com/repos/choderalab/yank/issues/261","id":113818800,"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},"created_at":"2015-06-20T20:49:23Z","updated_at":"2015-06-20T20:49:23Z","body":"I've determined that the atom selection for the alchemical region in the driver script isn't working correctly, so the bug must be somewhere in here:\r\nhttps://github.com/jchodera/yank/blob/fix-abl-example/examples/mhc-peptide-tcr/mhc-peptide-tcr.py#L277-L295"}}