{"action":"created","issue":{"url":"https://api.github.com/repos/MobleyLab/alchemical-setup/issues/4","labels_url":"https://api.github.com/repos/MobleyLab/alchemical-setup/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/MobleyLab/alchemical-setup/issues/4/comments","events_url":"https://api.github.com/repos/MobleyLab/alchemical-setup/issues/4/events","html_url":"https://github.com/MobleyLab/alchemical-setup/issues/4","id":115194326,"number":4,"title":"NameError: global name 'parametersB' is not defined","user":{"login":"camizanette","id":6915140,"avatar_url":"https://avatars.githubusercontent.com/u/6915140?v=3","gravatar_id":"","url":"https://api.github.com/users/camizanette","html_url":"https://github.com/camizanette","followers_url":"https://api.github.com/users/camizanette/followers","following_url":"https://api.github.com/users/camizanette/following{/other_user}","gists_url":"https://api.github.com/users/camizanette/gists{/gist_id}","starred_url":"https://api.github.com/users/camizanette/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/camizanette/subscriptions","organizations_url":"https://api.github.com/users/camizanette/orgs","repos_url":"https://api.github.com/users/camizanette/repos","events_url":"https://api.github.com/users/camizanette/events{/privacy}","received_events_url":"https://api.github.com/users/camizanette/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-11-05T02:17:27Z","updated_at":"2015-11-12T21:13:29Z","closed_at":null,"body":"I was using a different format of topologies files and I got this error saying the variable parametersB is not defined previously. The issue comes from Part IV, when it is processing the dihedrals and the top file format doesn't match with what the code is expecting, going to an exception in line 380. What I have noticed is acpype and parmed return different dihedrals functions types (9 and 1), and amb2gmx.pl returns the function type 3 (the one that works). Samples here: https://drive.google.com/folderview?id=0B5Hiv4aw8v8CWWU3N2ZVb2FsbWs&usp=sharing\r\nThere are two folders, one with topologies from Parmed and other from amb2gmx.pl.\r\nLet me know if it does not work.\r\n\r\nTraceback (most recent call last):\r\nFile \"../../local/alchemical-setup-master/alchemical-setup.py\", line 549, in \r\nbuildBonded() # Part IV.\r\nFile \"../../local/alchemical-setup-master/alchemical-setup.py\", line 429, in buildBonded\r\npostprocessDihedrals()\r\nFile \"../../local/alchemical-setup-master/alchemical-setup.py\", line 385, in postprocessDihedrals\r\nif l['parameters'][-1] != parametersB[-1]:\r\nNameError: global name 'parametersB' is not defined"},"comment":{"url":"https://api.github.com/repos/MobleyLab/alchemical-setup/issues/comments/156235259","html_url":"https://github.com/MobleyLab/alchemical-setup/issues/4#issuecomment-156235259","issue_url":"https://api.github.com/repos/MobleyLab/alchemical-setup/issues/4","id":156235259,"user":{"login":"FEPanalysis","id":9339661,"avatar_url":"https://avatars.githubusercontent.com/u/9339661?v=3","gravatar_id":"","url":"https://api.github.com/users/FEPanalysis","html_url":"https://github.com/FEPanalysis","followers_url":"https://api.github.com/users/FEPanalysis/followers","following_url":"https://api.github.com/users/FEPanalysis/following{/other_user}","gists_url":"https://api.github.com/users/FEPanalysis/gists{/gist_id}","starred_url":"https://api.github.com/users/FEPanalysis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/FEPanalysis/subscriptions","organizations_url":"https://api.github.com/users/FEPanalysis/orgs","repos_url":"https://api.github.com/users/FEPanalysis/repos","events_url":"https://api.github.com/users/FEPanalysis/events{/privacy}","received_events_url":"https://api.github.com/users/FEPanalysis/received_events","type":"User","site_admin":false},"created_at":"2015-11-12T21:13:29Z","updated_at":"2015-11-12T21:13:29Z","body":"December is the month when I will have a chance to look at it.\r\n"}}