{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/constph-openmm/issues/45","repository_url":"https://api.github.com/repos/choderalab/constph-openmm","labels_url":"https://api.github.com/repos/choderalab/constph-openmm/issues/45/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/constph-openmm/issues/45/comments","events_url":"https://api.github.com/repos/choderalab/constph-openmm/issues/45/events","html_url":"https://github.com/choderalab/constph-openmm/issues/45","id":158223137,"number":45,"title":"Debug simulation crashes","user":{"login":"bas-rustenburg","id":3977731,"avatar_url":"https://avatars.githubusercontent.com/u/3977731?v=3","gravatar_id":"","url":"https://api.github.com/users/bas-rustenburg","html_url":"https://github.com/bas-rustenburg","followers_url":"https://api.github.com/users/bas-rustenburg/followers","following_url":"https://api.github.com/users/bas-rustenburg/following{/other_user}","gists_url":"https://api.github.com/users/bas-rustenburg/gists{/gist_id}","starred_url":"https://api.github.com/users/bas-rustenburg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bas-rustenburg/subscriptions","organizations_url":"https://api.github.com/users/bas-rustenburg/orgs","repos_url":"https://api.github.com/users/bas-rustenburg/repos","events_url":"https://api.github.com/users/bas-rustenburg/events{/privacy}","received_events_url":"https://api.github.com/users/bas-rustenburg/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"bas-rustenburg","id":3977731,"avatar_url":"https://avatars.githubusercontent.com/u/3977731?v=3","gravatar_id":"","url":"https://api.github.com/users/bas-rustenburg","html_url":"https://github.com/bas-rustenburg","followers_url":"https://api.github.com/users/bas-rustenburg/followers","following_url":"https://api.github.com/users/bas-rustenburg/following{/other_user}","gists_url":"https://api.github.com/users/bas-rustenburg/gists{/gist_id}","starred_url":"https://api.github.com/users/bas-rustenburg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bas-rustenburg/subscriptions","organizations_url":"https://api.github.com/users/bas-rustenburg/orgs","repos_url":"https://api.github.com/users/bas-rustenburg/repos","events_url":"https://api.github.com/users/bas-rustenburg/events{/privacy}","received_events_url":"https://api.github.com/users/bas-rustenburg/received_events","type":"User","site_admin":false},"assignees":[{"login":"bas-rustenburg","id":3977731,"avatar_url":"https://avatars.githubusercontent.com/u/3977731?v=3","gravatar_id":"","url":"https://api.github.com/users/bas-rustenburg","html_url":"https://github.com/bas-rustenburg","followers_url":"https://api.github.com/users/bas-rustenburg/followers","following_url":"https://api.github.com/users/bas-rustenburg/following{/other_user}","gists_url":"https://api.github.com/users/bas-rustenburg/gists{/gist_id}","starred_url":"https://api.github.com/users/bas-rustenburg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bas-rustenburg/subscriptions","organizations_url":"https://api.github.com/users/bas-rustenburg/orgs","repos_url":"https://api.github.com/users/bas-rustenburg/repos","events_url":"https://api.github.com/users/bas-rustenburg/events{/privacy}","received_events_url":"https://api.github.com/users/bas-rustenburg/received_events","type":"User","site_admin":false}],"milestone":null,"comments":6,"created_at":"2016-06-02T19:42:33Z","updated_at":"2016-10-06T16:11:53Z","closed_at":null,"body":"As a reminder to do some debugging, I'm logging some simulations that failed, in case the issues are related to the code.\r\n\r\nFailed simulations that will need debugging. \r\n- ./ALK-Alectinib/3AOX_fixed_ph7.4.pdb.ligand/failed.txt failed fast\r\n- ./VEGFR1-Axitinib/4AG8_fixed_ph7.4.pdb.ligand/failed.txt failed fast\r\n- ./ALK-Crizotinib/2XP2_fixed_ph7.4.pdb.ligand/failed.txt failed fast\r\n- ./ALK-Crizotinib/2XP2_fixed_ph7.4.pdb.apo/failed.txt failed fast\r\n- ./MET-Crizotinib/2WGJ_fixed_ph7.4.pdb.ligand/failed.txt failed fast\r\n- ./BCRABL-Dasatinib/2GQG_fixed_ph7.4.pdb.ligand/failed.txt failed fast\r\n- ./VEGFR1-Regorafenib/2QU5_fixed_ph7.4.pdb.ligand/failed.txt failed fast\r\n- _./ALK-Crizotinib/2YFX_fixed_ph7.4.pdb.ligand/failed.txt_   late failure, restarted. \r\n- _./BCRABL-Imatinib/3PYY_fixed_ph7.4.pdb.ligand/failed.txt_ late failure, restarted, failed again\r\n- _./VEGFR1-Axitinib/4AGC_fixed_ph7.4.pdb.ligand/failed.txt_ late failure, restarted\r\n- _./BRAF-Dabrafenib/5CSW_fixed_ph7.4.pdb.ligand/failed.txt late failure_\r\n- _./BRAF-Dabrafenib/5HIE_fixed_ph7.4.pdb.ligand/failed.txt late failure_\r\n- _./BCRABL-Imatinib/2HYY_fixed_ph7.4.pdb.ligand/failed.txt_ late failure\r\n- _./BRAF-Dabrafenib/4XV2_fixed_ph7.4.pdb.ligand/failed.txt_ late failure\r\n\r\nList of all simulations, failed ones in **bold**\r\n\r\n- **./ALK-Alectinib/3AOX_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- ./ALK-Alectinib/3AOX_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- **./VEGFR1-Axitinib/4AG8_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- **./VEGFR1-Axitinib/4AGC_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- ./VEGFR1-Axitinib/4AG8_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- ./VEGFR1-Axitinib/4AGC_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- **./ALK-Crizotinib/2XP2_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- _**./ALK-Crizotinib/2YFX_fixed_ph7.4.pdb.ligand/trajectory.dcd**_\r\n- ./ALK-Crizotinib/4ANQ_fixed_ph7.4.pdb.ligand/trajectory.dcd\r\n- ./ALK-Crizotinib/4ANS_fixed_ph7.4.pdb.ligand/trajectory.dcd\r\n- **./ALK-Crizotinib/2XP2_fixed_ph7.4.pdb.apo/trajectory.dcd**\r\n- ./ALK-Crizotinib/2YFX_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- ./ALK-Crizotinib/4ANQ_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- ./ALK-Crizotinib/4ANS_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- **./MET-Crizotinib/2WGJ_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- ./MET-Crizotinib/2WGJ_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- **./BRAF-Dabrafenib/4XV2_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- **./BRAF-Dabrafenib/5CSW_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- **./BRAF-Dabrafenib/5HIE_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- ./BRAF-Dabrafenib/4XV2_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- ./BRAF-Dabrafenib/5CSW_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- ./BRAF-Dabrafenib/5HIE_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- **./BCRABL-Dasatinib/2GQG_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- ./BCRABL-Dasatinib/4XEY_fixed_ph7.4.pdb.ligand/trajectory.dcd\r\n- ./BCRABL-Dasatinib/2GQG_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- ./BCRABL-Dasatinib/4XEY_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- ./BCRABL-Imatinib/2HYY_fixed_ph7.4.pdb.ligand/trajectory.dcd\r\n- **./BCRABL-Imatinib/3PYY_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- **./BCRABL-Imatinib/2HYY_fixed_ph7.4.pdb.apo/trajectory.dcd**\r\n- ./BCRABL-Imatinib/3PYY_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n- **./VEGFR1-Regorafenib/2QU5_fixed_ph7.4.pdb.ligand/trajectory.dcd**\r\n- ./VEGFR1-Regorafenib/2QU5_fixed_ph7.4.pdb.apo/trajectory.dcd\r\n"},"comment":{"url":"https://api.github.com/repos/choderalab/constph-openmm/issues/comments/252011154","html_url":"https://github.com/choderalab/constph-openmm/issues/45#issuecomment-252011154","issue_url":"https://api.github.com/repos/choderalab/constph-openmm/issues/45","id":252011154,"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":"2016-10-06T16:11:53Z","updated_at":"2016-10-06T16:11:53Z","body":"We are looking into more robust loop building alternatives for these\nstructures. At the very least, we will need to see how robust the MCCE\ncalculations are to the loop modeling strategy on a few specific cases.\n"}}
{"actor":{"display_login":"jchodera"}}