{"action":"created","issue":{"url":"https://api.github.com/repos/ParmEd/ParmEd/issues/459","labels_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/459/labels{/name}","comments_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/459/comments","events_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/459/events","html_url":"https://github.com/ParmEd/ParmEd/issues/459","id":112253625,"number":459,"title":"Conversion error for SPC/E water box from GROMACS->Amber","user":{"login":"mrshirts","id":4274132,"avatar_url":"https://avatars.githubusercontent.com/u/4274132?v=3","gravatar_id":"","url":"https://api.github.com/users/mrshirts","html_url":"https://github.com/mrshirts","followers_url":"https://api.github.com/users/mrshirts/followers","following_url":"https://api.github.com/users/mrshirts/following{/other_user}","gists_url":"https://api.github.com/users/mrshirts/gists{/gist_id}","starred_url":"https://api.github.com/users/mrshirts/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mrshirts/subscriptions","organizations_url":"https://api.github.com/users/mrshirts/orgs","repos_url":"https://api.github.com/users/mrshirts/repos","events_url":"https://api.github.com/users/mrshirts/events{/privacy}","received_events_url":"https://api.github.com/users/mrshirts/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":29,"created_at":"2015-10-19T23:29:22Z","updated_at":"2015-10-21T01:46:17Z","closed_at":null,"body":"I'm running ParmEd on a GROMACS SPC/E box (for unit tests in InterMol).  When run in sander, the converted files give a segmentation fault; it's not clear where it's occurring exactly (the mdout says, but it's not clear to me what the issue might be).\r\n\r\nI'm sending files to Jason as an email since I do not have write permission for the repository to attach the files here.\r\n\r\nSending:\r\n\r\n1. sander mdout\r\n2. gromacs .top\r\n3. gromacs .gro\r\n4. amber .prmtop\r\n4. amber .rst7\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/ParmEd/ParmEd/issues/comments/149754735","html_url":"https://github.com/ParmEd/ParmEd/issues/459#issuecomment-149754735","issue_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/459","id":149754735,"user":{"login":"mrshirts","id":4274132,"avatar_url":"https://avatars.githubusercontent.com/u/4274132?v=3","gravatar_id":"","url":"https://api.github.com/users/mrshirts","html_url":"https://github.com/mrshirts","followers_url":"https://api.github.com/users/mrshirts/followers","following_url":"https://api.github.com/users/mrshirts/following{/other_user}","gists_url":"https://api.github.com/users/mrshirts/gists{/gist_id}","starred_url":"https://api.github.com/users/mrshirts/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mrshirts/subscriptions","organizations_url":"https://api.github.com/users/mrshirts/orgs","repos_url":"https://api.github.com/users/mrshirts/repos","events_url":"https://api.github.com/users/mrshirts/events{/privacy}","received_events_url":"https://api.github.com/users/mrshirts/received_events","type":"User","site_admin":false},"created_at":"2015-10-21T01:46:17Z","updated_at":"2015-10-21T01:46:17Z","body":"Right, I'm just mentioning that as a difference that other programs handle.  If you do the imaging first with a 20 A box, then the water molecules all look normal."}}