{"action":"created","issue":{"url":"https://api.github.com/repos/ParmEd/ParmEd/issues/626","repository_url":"https://api.github.com/repos/ParmEd/ParmEd","labels_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/626/labels{/name}","comments_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/626/comments","events_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/626/events","html_url":"https://github.com/ParmEd/ParmEd/issues/626","id":137632801,"number":626,"title":"AT14 parmed assigns incorrect LJ 12-6-4 C COEFF terms","user":{"login":"cbergonzo","id":17572790,"avatar_url":"https://avatars.githubusercontent.com/u/17572790?v=3","gravatar_id":"","url":"https://api.github.com/users/cbergonzo","html_url":"https://github.com/cbergonzo","followers_url":"https://api.github.com/users/cbergonzo/followers","following_url":"https://api.github.com/users/cbergonzo/following{/other_user}","gists_url":"https://api.github.com/users/cbergonzo/gists{/gist_id}","starred_url":"https://api.github.com/users/cbergonzo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cbergonzo/subscriptions","organizations_url":"https://api.github.com/users/cbergonzo/orgs","repos_url":"https://api.github.com/users/cbergonzo/repos","events_url":"https://api.github.com/users/cbergonzo/events{/privacy}","received_events_url":"https://api.github.com/users/cbergonzo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-03-01T17:06:40Z","updated_at":"2016-03-02T02:08:40Z","closed_at":null,"body":"Hi Jason,\r\n\r\nUsing parmed from AT 14 and the more recent version 2.2, my results for the C coefficient terms for 12-6-4 potential simulations differed. \r\nWhen I use AT 14 parmed, I get incorrect C4 terms when I use either current GIT lj_1264_pol.dat file or AT14 lj_1264_pol.dat.\r\nWhen I use parmed version 2.2 with the current GIT lj_1264_pol.dat, I get what seems like the correct C4 terms. \r\nWhen I use parmed version 2.2 with AT 14 lj_1264_pol.dat, I get an error which says CI/CT atom types have the same pol term but different vdW terms, which they do, so this error seems correct.\r\n\r\nThe differences are as follows:\r\n![image](https://cloud.githubusercontent.com/assets/17572790/13434784/604fb42c-df94-11e5-94a0-c87aa3581ad7.png)\r\n\r\nThe Cl/Cl- error is due to two different pol factors for Cl and Cl-, which is confusing since these parmtops were built the same way with the same Cl- ions (unless the Cl- ions were reamed somewhere, maybe in atomic_ions.lib?). The HO was zeroed to match the zero vdW terms for the current git. It seems like CI/CT defaulted to C* when the different pol factors couldn't be resolved. I'm not sure where the water C coefficients came from, or why K+ wasn't assigned at all.\r\n\r\nUsing current versions of both the pol file and parmed, I get what I *think* are correct C coefficient values (except for the Cl/Cl- issue which I have to sort out). Was the AT14 bug known?\r\n\r\n-Christina\r\n\r\n[ForJason-1264.xlsx](https://github.com/ParmEd/ParmEd/files/153182/ForJason-1264.xlsx)"},"comment":{"url":"https://api.github.com/repos/ParmEd/ParmEd/issues/comments/191018973","html_url":"https://github.com/ParmEd/ParmEd/issues/626#issuecomment-191018973","issue_url":"https://api.github.com/repos/ParmEd/ParmEd/issues/626","id":191018973,"user":{"login":"swails","id":779022,"avatar_url":"https://avatars.githubusercontent.com/u/779022?v=3","gravatar_id":"","url":"https://api.github.com/users/swails","html_url":"https://github.com/swails","followers_url":"https://api.github.com/users/swails/followers","following_url":"https://api.github.com/users/swails/following{/other_user}","gists_url":"https://api.github.com/users/swails/gists{/gist_id}","starred_url":"https://api.github.com/users/swails/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/swails/subscriptions","organizations_url":"https://api.github.com/users/swails/orgs","repos_url":"https://api.github.com/users/swails/repos","events_url":"https://api.github.com/users/swails/events{/privacy}","received_events_url":"https://api.github.com/users/swails/received_events","type":"User","site_admin":false},"created_at":"2016-03-02T02:08:40Z","updated_at":"2016-03-02T02:08:40Z","body":"So I know that at some point, Pengfei changed the parameters for hydroxyl H's so that the C4 term was 0.  So the Mg2+/HO and Mg2+/HW changes are what I expect.  CI,CT with Mg2+ I'm not sure what happened there, but I suspect it's because Pengfei changed some of the standard parameters.  I also know that dual ions were fixed in the current git version. So Mg2+/K+ should *not* be zero, and only was because the K+->Mg2+ term (which was zero because the K+ term was 0) overwrote the Mg2+->K+ term (which was, correctly, non-zero) -- #374 is the PR that fixed this.\r\n\r\nPinging @pengfeili1, since he should hopefully have more definitive answers.  But rows 1, 3, and 6 I fully expected to be different, and current parmed/current pol is the intended behavior."}}