{"action":"opened","issue":{"url":"https://api.github.com/repos/open-forcefield-group/smirff99Frosst/issues/14","repository_url":"https://api.github.com/repos/open-forcefield-group/smirff99Frosst","labels_url":"https://api.github.com/repos/open-forcefield-group/smirff99Frosst/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/open-forcefield-group/smirff99Frosst/issues/14/comments","events_url":"https://api.github.com/repos/open-forcefield-group/smirff99Frosst/issues/14/events","html_url":"https://github.com/open-forcefield-group/smirff99Frosst/issues/14","id":210985341,"number":14,"title":"Investigating generic parameters assigned to DrugBank Molecules","user":{"login":"bannanc","id":11968541,"avatar_url":"https://avatars0.githubusercontent.com/u/11968541?v=3","gravatar_id":"","url":"https://api.github.com/users/bannanc","html_url":"https://github.com/bannanc","followers_url":"https://api.github.com/users/bannanc/followers","following_url":"https://api.github.com/users/bannanc/following{/other_user}","gists_url":"https://api.github.com/users/bannanc/gists{/gist_id}","starred_url":"https://api.github.com/users/bannanc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bannanc/subscriptions","organizations_url":"https://api.github.com/users/bannanc/orgs","repos_url":"https://api.github.com/users/bannanc/repos","events_url":"https://api.github.com/users/bannanc/events{/privacy}","received_events_url":"https://api.github.com/users/bannanc/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-03-01T05:42:50Z","updated_at":"2017-03-01T05:42:50Z","closed_at":null,"body":"In connection with the Mobley Group undergraduate project [off-ffcompare](https://github.com/MobleyLab/off-ffcompare) I've been looking at how SMIRNOFF99Frosst types the molecules in DrugBank. Below I'll list in detail, what I'm finding, but the most surprising seems to be that for torsions some ethers seem to get assigned the generic ('t1') parameter. I'm haven't spent much time investigating why this might be happening (i.e. I haven't opened the ffxml or the \"smirffishFrcmod\" files yet)\r\n\r\n***Non-Bonding***\r\nWe're missing Boron and Silicon (and helium...) those are the three atoms that get 'n1' `[*:1]` the generic non-bonding parameter. I don't know why, but Helium as a single atom is in the DrugBank database. There are a total of 19 molecules with at least one of those atoms\r\n\r\n***Bonds***\r\nExcluding Silicon and boron, here are the types of functional groups being assigned 'b1' `[*:1]~[*:2]`\r\nThere are 81 molecules with at least one generic bond. Most have a carbonyl like group with sulfur (C=S)\r\n\r\nHere's the full list of bonds we seem to be missing\r\n* Sulfur\r\n    - S=0\r\n         - in a group with the shape *CX4-S(=O)=O the sulfur has an unpaired electron\r\n    - C=S\r\n        - Most of these were like a carbonyl group, but one was C=S-N\r\n    - P-S\r\n\r\n* Phosphorous\r\n    - P-Cl\r\n    - P-H\r\n\r\n* Nitrile Carbon\r\n    - C(nitrile)#N+1-CX4\r\n    - C(nitrile)-S\r\n    - C(nitrile)-I\r\n\r\n* Weird Cases\r\n    - N-Br\r\n         - I don't think this is common, but we should probably catch it\r\n    - in CO2 the C=0 bonds aren’t typed?\r\n         - I'm guessing this is because carbonyl carbons are probably written as [#6X3]=[#8] and the carbon dioxide carbon isn't trivalent, but I'm not entirely sure\r\n    - in O2 the O=O bond, but that is literately the only molecule where you’ll see that bond\r\n\r\n***Angles***\r\nThere aren't many here, only 3 molecules with the generic angle 'a1' `[*:1]~[*:2]~[*:3]`, I once again skipped any molecules with Boron or Silicon. \r\n\r\n* Sulfur\r\n    - [#6X3]=[#16X2]-[#7]\r\n        - Same as the weird C=S bond case above\r\n    - [#8]=[#16X2]-[#6X4]\r\n        - This is an oxygen double bonded to a divalent sulfur bound to a tetrahedral carbon\r\n* Nitrogen \r\n    - [#6X2]#[#7+1]-[#6X4]\r\n         - So this is a nitrile group with a positive charge on the nitrogen so it has the shape R-C#N+-R \r\n\r\n***Torsions***\r\nThere are 2499 molecules of the 6122 being tested from the DrugBank molecules database that are assigned at least one generic torsion 't1' `[*:1]~[*:2]~[*:3]~[*:4]`. That is a ridiculous number!!!\r\n\r\nA LOT of them are ethers where the torsion getting the generic is in the form \r\n[#1:1]-[#6X4]-[#8X2]-[#6]\r\nhydrogen - tetravalent carbon - oxygen - carbon\r\nthe last carbon is sometimes tetrahedral and sometimes aromatic. We had these torsions even in the AlkEthOH SMIRFF so I don't know why they aren't being typed now. I'm going to look more closely at some of the individual molecules later this week. "}}
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