{"action":"closed","issue":{"url":"https://api.github.com/repos/Acellera/htmd/issues/188","repository_url":"https://api.github.com/repos/Acellera/htmd","labels_url":"https://api.github.com/repos/Acellera/htmd/issues/188/labels{/name}","comments_url":"https://api.github.com/repos/Acellera/htmd/issues/188/comments","events_url":"https://api.github.com/repos/Acellera/htmd/issues/188/events","html_url":"https://github.com/Acellera/htmd/issues/188","id":189695080,"number":188,"title":"Parameterize atom type naming inconsistency","user":{"login":"katkovs","id":23500283,"avatar_url":"https://avatars.githubusercontent.com/u/23500283?v=3","gravatar_id":"","url":"https://api.github.com/users/katkovs","html_url":"https://github.com/katkovs","followers_url":"https://api.github.com/users/katkovs/followers","following_url":"https://api.github.com/users/katkovs/following{/other_user}","gists_url":"https://api.github.com/users/katkovs/gists{/gist_id}","starred_url":"https://api.github.com/users/katkovs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/katkovs/subscriptions","organizations_url":"https://api.github.com/users/katkovs/orgs","repos_url":"https://api.github.com/users/katkovs/repos","events_url":"https://api.github.com/users/katkovs/events{/privacy}","received_events_url":"https://api.github.com/users/katkovs/received_events","type":"User","site_admin":false},"labels":[{"id":397041878,"url":"https://api.github.com/repos/Acellera/htmd/labels/Parameterize","name":"Parameterize","color":"d4c5f9","default":false}],"state":"closed","locked":false,"assignee":{"login":"mj-harvey","id":7896589,"avatar_url":"https://avatars.githubusercontent.com/u/7896589?v=3","gravatar_id":"","url":"https://api.github.com/users/mj-harvey","html_url":"https://github.com/mj-harvey","followers_url":"https://api.github.com/users/mj-harvey/followers","following_url":"https://api.github.com/users/mj-harvey/following{/other_user}","gists_url":"https://api.github.com/users/mj-harvey/gists{/gist_id}","starred_url":"https://api.github.com/users/mj-harvey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mj-harvey/subscriptions","organizations_url":"https://api.github.com/users/mj-harvey/orgs","repos_url":"https://api.github.com/users/mj-harvey/repos","events_url":"https://api.github.com/users/mj-harvey/events{/privacy}","received_events_url":"https://api.github.com/users/mj-harvey/received_events","type":"User","site_admin":false},"assignees":[{"login":"mj-harvey","id":7896589,"avatar_url":"https://avatars.githubusercontent.com/u/7896589?v=3","gravatar_id":"","url":"https://api.github.com/users/mj-harvey","html_url":"https://github.com/mj-harvey","followers_url":"https://api.github.com/users/mj-harvey/followers","following_url":"https://api.github.com/users/mj-harvey/following{/other_user}","gists_url":"https://api.github.com/users/mj-harvey/gists{/gist_id}","starred_url":"https://api.github.com/users/mj-harvey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mj-harvey/subscriptions","organizations_url":"https://api.github.com/users/mj-harvey/orgs","repos_url":"https://api.github.com/users/mj-harvey/repos","events_url":"https://api.github.com/users/mj-harvey/events{/privacy}","received_events_url":"https://api.github.com/users/mj-harvey/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/Acellera/htmd/milestones/3","html_url":"https://github.com/Acellera/htmd/milestones/1.6.0%20(stable)","labels_url":"https://api.github.com/repos/Acellera/htmd/milestones/3/labels","id":1815289,"number":3,"title":"1.6.0 (stable)","description":"","creator":{"login":"j3mdamas","id":10810178,"avatar_url":"https://avatars.githubusercontent.com/u/10810178?v=3","gravatar_id":"","url":"https://api.github.com/users/j3mdamas","html_url":"https://github.com/j3mdamas","followers_url":"https://api.github.com/users/j3mdamas/followers","following_url":"https://api.github.com/users/j3mdamas/following{/other_user}","gists_url":"https://api.github.com/users/j3mdamas/gists{/gist_id}","starred_url":"https://api.github.com/users/j3mdamas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/j3mdamas/subscriptions","organizations_url":"https://api.github.com/users/j3mdamas/orgs","repos_url":"https://api.github.com/users/j3mdamas/repos","events_url":"https://api.github.com/users/j3mdamas/events{/privacy}","received_events_url":"https://api.github.com/users/j3mdamas/received_events","type":"User","site_admin":false},"open_issues":16,"closed_issues":24,"state":"open","created_at":"2016-06-08T09:53:17Z","updated_at":"2016-11-17T12:55:36Z","due_on":"2017-01-13T00:00:00Z","closed_at":null},"comments":5,"created_at":"2016-11-16T12:53:33Z","updated_at":"2016-11-17T12:55:36Z","closed_at":"2016-11-17T12:55:36Z","body":"Hi,\r\n\r\nI am using htmd version 1.5.4 to parameterize a molecule with GAFF. The calculations run fine, but the new atom types in the resulting frcmod and mol2 files are differently named (za,zb,zc... vs. cax0, cax1, cex0...). This prevents leap from successfully creating the prmtop topology file. One would have to guess which atom types from the frcmod file correspond to which atoms in the molecule.  \r\nI also noticed that in the dihedral plots, the original MM dihedral is not shown correctly (it is plotted identical to the fitted one), but I don't know if this is related to the naming issue.\r\n\r\nVersion 1.5.1 does not have this problem (atom types are named za,zb,zc... in both, mol2 and frcmod files, and the the original MM dihedral is plotted fine). \r\n\r\nLet me know if you need any more information or some example files.\r\n\r\nThanks,\r\nKalina\r\n\r\n\r\n       "}}
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