{"action":"created","issue":{"url":"https://api.github.com/repos/Acellera/htmd/issues/13","repository_url":"https://api.github.com/repos/Acellera/htmd","labels_url":"https://api.github.com/repos/Acellera/htmd/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/Acellera/htmd/issues/13/comments","events_url":"https://api.github.com/repos/Acellera/htmd/issues/13/events","html_url":"https://github.com/Acellera/htmd/issues/13","id":147465283,"number":13,"title":"caps in amber","user":{"login":"noeliaferruz","id":12035024,"avatar_url":"https://avatars.githubusercontent.com/u/12035024?v=3","gravatar_id":"","url":"https://api.github.com/users/noeliaferruz","html_url":"https://github.com/noeliaferruz","followers_url":"https://api.github.com/users/noeliaferruz/followers","following_url":"https://api.github.com/users/noeliaferruz/following{/other_user}","gists_url":"https://api.github.com/users/noeliaferruz/gists{/gist_id}","starred_url":"https://api.github.com/users/noeliaferruz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/noeliaferruz/subscriptions","organizations_url":"https://api.github.com/users/noeliaferruz/orgs","repos_url":"https://api.github.com/users/noeliaferruz/repos","events_url":"https://api.github.com/users/noeliaferruz/events{/privacy}","received_events_url":"https://api.github.com/users/noeliaferruz/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-04-11T15:30:09Z","updated_at":"2016-04-11T15:39:25Z","closed_at":null,"body":"Hi all,\r\n\r\nGot this error when building an amber system. It's a bit strange because I think this same system worked a couple of weeks ago and also works in charmm. The protein I'm using is 5hd0.pdb and saving chain A (attached solvated molecule a txt file, pdbs aren't supported here).\r\n\r\n[solvated.txt](https://github.com/Acellera/htmd/files/213285/solvated.txt)\r\n\r\n2016-04-11 10:59:09,963 - htmd.builder.amber - INFO - Converting CHARMM membranes to AMBER.\r\nTraceback (most recent call last):\r\n  File \"/hpc/grid/wip_cmg_wwmc/workspace/groups/neuro_cc/acellera/scripts/md/globular/md_apo/1.build.py\", line 51, in <module>\r\n    builtamber= amber.build( solvated, ff=ffs, outdir='build')\r\n  File \"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/htmd/builder/amber.py\", line 109, in build\r\n    _applyCaps(mol, caps)\r\n  File \"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/htmd/builder/amber.py\", line 216, in _applyCaps\r\n    raise AssertionError('Segment {}, resid {} should have either one H2 or one HT2 atom. Cannot cap.'.format(seg, np.min(resids)))\r\nAssertionError: Segment P0, resid 58 should have either one H2 or one HT2 atom. Cannot cap.\r\n\r\nThanks"},"comment":{"url":"https://api.github.com/repos/Acellera/htmd/issues/comments/208407131","html_url":"https://github.com/Acellera/htmd/issues/13#issuecomment-208407131","issue_url":"https://api.github.com/repos/Acellera/htmd/issues/13","id":208407131,"user":{"login":"stefdoerr","id":7935362,"avatar_url":"https://avatars.githubusercontent.com/u/7935362?v=3","gravatar_id":"","url":"https://api.github.com/users/stefdoerr","html_url":"https://github.com/stefdoerr","followers_url":"https://api.github.com/users/stefdoerr/followers","following_url":"https://api.github.com/users/stefdoerr/following{/other_user}","gists_url":"https://api.github.com/users/stefdoerr/gists{/gist_id}","starred_url":"https://api.github.com/users/stefdoerr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stefdoerr/subscriptions","organizations_url":"https://api.github.com/users/stefdoerr/orgs","repos_url":"https://api.github.com/users/stefdoerr/repos","events_url":"https://api.github.com/users/stefdoerr/events{/privacy}","received_events_url":"https://api.github.com/users/stefdoerr/received_events","type":"User","site_admin":false},"created_at":"2016-04-11T15:39:25Z","updated_at":"2016-04-11T15:39:25Z","body":"I guess we should add that to the error message to point people in the right direction."}}