{"action":"created","issue":{"url":"https://api.github.com/repos/Acellera/htmd/issues/9","repository_url":"https://api.github.com/repos/Acellera/htmd","labels_url":"https://api.github.com/repos/Acellera/htmd/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/Acellera/htmd/issues/9/comments","events_url":"https://api.github.com/repos/Acellera/htmd/issues/9/events","html_url":"https://github.com/Acellera/htmd/issues/9","id":146261452,"number":9,"title":"Parametrise: run(): Step [input] did not produce the expected output","user":{"login":"ggutierrez-bio","id":18290133,"avatar_url":"https://avatars.githubusercontent.com/u/18290133?v=3","gravatar_id":"","url":"https://api.github.com/users/ggutierrez-bio","html_url":"https://github.com/ggutierrez-bio","followers_url":"https://api.github.com/users/ggutierrez-bio/followers","following_url":"https://api.github.com/users/ggutierrez-bio/following{/other_user}","gists_url":"https://api.github.com/users/ggutierrez-bio/gists{/gist_id}","starred_url":"https://api.github.com/users/ggutierrez-bio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ggutierrez-bio/subscriptions","organizations_url":"https://api.github.com/users/ggutierrez-bio/orgs","repos_url":"https://api.github.com/users/ggutierrez-bio/repos","events_url":"https://api.github.com/users/ggutierrez-bio/events{/privacy}","received_events_url":"https://api.github.com/users/ggutierrez-bio/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Acellera/htmd/labels/bug:high","name":"bug:high","color":"fc2929"}],"state":"open","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},"milestone":{"url":"https://api.github.com/repos/Acellera/htmd/milestones/1","html_url":"https://github.com/Acellera/htmd/milestones/v1.1.0","labels_url":"https://api.github.com/repos/Acellera/htmd/milestones/1/labels","id":1722901,"number":1,"title":"v1.1.0","description":"New HTMD stable release","creator":{"login":"giadefa","id":7776826,"avatar_url":"https://avatars.githubusercontent.com/u/7776826?v=3","gravatar_id":"","url":"https://api.github.com/users/giadefa","html_url":"https://github.com/giadefa","followers_url":"https://api.github.com/users/giadefa/followers","following_url":"https://api.github.com/users/giadefa/following{/other_user}","gists_url":"https://api.github.com/users/giadefa/gists{/gist_id}","starred_url":"https://api.github.com/users/giadefa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/giadefa/subscriptions","organizations_url":"https://api.github.com/users/giadefa/orgs","repos_url":"https://api.github.com/users/giadefa/repos","events_url":"https://api.github.com/users/giadefa/events{/privacy}","received_events_url":"https://api.github.com/users/giadefa/received_events","type":"User","site_admin":false},"open_issues":4,"closed_issues":0,"state":"open","created_at":"2016-04-21T14:17:38Z","updated_at":"2016-05-10T14:16:24Z","due_on":"2016-05-31T22:00:00Z","closed_at":null},"comments":2,"created_at":"2016-04-06T10:07:21Z","updated_at":"2016-05-10T14:16:36Z","closed_at":null,"body":"Hi,\r\nI wanted to try parameterise, so I installed it and set up a simple test system, but when I trie to run it (from command line or within a python script) it dies with the error in the title.\r\nHere's what I did:\r\n\r\ninstalled through\r\n\r\n`conda install parametrise -c acellera`\r\n\r\nthe molecule file (3mpr_ac.mol2) and the input file (pjob) are attached below.\r\npjob contains this:\r\n\r\n```\r\nJobName 3mpr_test\r\nFileName 3mpr_ac.mol2\r\nNetCharge 0\r\n```\r\ncalling parameterise this way\r\n\r\n`parameterise --input pjob`\r\n\r\nreturns this: \r\n```\r\nVideos from the HTMD2015 workshops are available on the Acellera youtube channel: https://www.youtube.com/user/acelleralive\r\n\r\nYou are on the latest HTMD version (1.0.8).\r\n\r\n === Parameterise 2016 ===\r\n\r\n      (c) Acellera \r\n        AsymmetricTorsion False\r\n                    Debug False\r\n                   E14FAC 1.0\r\n               Equivalent None\r\n            ExecutionMode Inline\r\n                 FileName 3mpr_ac.mol2\r\n               FixCharges None\r\n             GAUSS_SCRDIR /tmp\r\n                  JobName 3mpr_test\r\n                   MEMORY 8\r\n               MaxTorsion 25\r\n                    Model Nonpolar\r\n             Multiplicity 1\r\n                   NCORES 8\r\n                NetCharge 0\r\n                  Neutral None\r\n                 Torsions []\r\n       w_H_Donor_Acceptor 1.0\r\n                  w_alpha 0.4\r\n                 w_charge 3.0\r\n                  w_thole 0.2\r\n            w_water_E_min 0.4\r\n            w_water_R_min 8.0\r\n                 wd_alpha 0.4\r\n                wd_charge 1.0\r\n                 wd_thole 0.2\r\n           wd_water_E_min 0.4\r\n           wd_water_R_min 8.0\r\n\r\nRunning step [000] [input]\r\n\r\n Failed to run parameterisation : run(): Step [input] did not produce the expected output: ['ligand.xyz'] in directory /home/ggutierrez/.htmd/gaamp/3mpr_test/000-input\r\n```\r\nadditional note: gaussian is correctly installed in its version 09 with all the necessary environment variables set up, but the value of GAUSS_SCRDIR in this output doesn't match the one i configured.\r\n( /tmp vs /data3/g09scr )\r\n\r\nam I missing something here?\r\n\r\n[files.zip](https://github.com/Acellera/htmd/files/206147/files.zip)\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/Acellera/htmd/issues/comments/218170989","html_url":"https://github.com/Acellera/htmd/issues/9#issuecomment-218170989","issue_url":"https://api.github.com/repos/Acellera/htmd/issues/9","id":218170989,"user":{"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},"created_at":"2016-05-10T14:16:36Z","updated_at":"2016-05-10T14:16:36Z","body":"Hi,\r\n\r\nApologies for the slow follow-up. Please could you list the files in the directory:\r\n\r\n$HOME/.htmd/gaamp/3mpr_test/000-input/ \r\n\r\nAlso, please do a conda update htmd -y ; conda install htmdbabel ; conda update htmdbabel and retry\r\n\r\nMatt\r\n"}}