{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/yank/issues/248","repository_url":"https://api.github.com/repos/choderalab/yank","labels_url":"https://api.github.com/repos/choderalab/yank/issues/248/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/yank/issues/248/comments","events_url":"https://api.github.com/repos/choderalab/yank/issues/248/events","html_url":"https://github.com/choderalab/yank/issues/248","id":87438690,"number":248,"title":"Plan general setup workflow for protein+ligand simulations","user":{"login":"davidlmobley","id":7132257,"avatar_url":"https://avatars.githubusercontent.com/u/7132257?v=3","gravatar_id":"","url":"https://api.github.com/users/davidlmobley","html_url":"https://github.com/davidlmobley","followers_url":"https://api.github.com/users/davidlmobley/followers","following_url":"https://api.github.com/users/davidlmobley/following{/other_user}","gists_url":"https://api.github.com/users/davidlmobley/gists{/gist_id}","starred_url":"https://api.github.com/users/davidlmobley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidlmobley/subscriptions","organizations_url":"https://api.github.com/users/davidlmobley/orgs","repos_url":"https://api.github.com/users/davidlmobley/repos","events_url":"https://api.github.com/users/davidlmobley/events{/privacy}","received_events_url":"https://api.github.com/users/davidlmobley/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/choderalab/yank/milestones/2","html_url":"https://github.com/choderalab/yank/milestones/icebox","labels_url":"https://api.github.com/repos/choderalab/yank/milestones/2/labels","id":867831,"number":2,"title":"icebox","description":"","creator":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"open_issues":33,"closed_issues":0,"state":"open","created_at":"2014-11-15T19:16:46Z","updated_at":"2016-06-07T22:40:56Z","due_on":null,"closed_at":null},"comments":14,"created_at":"2015-06-11T18:23:59Z","updated_at":"2016-06-07T22:41:10Z","closed_at":null,"body":"Related to #247 - currently Yank has systembuilder, which probably ought to be split off into a more general-purpose tool that will be useful aside from just for Yank workflows (i.e. setup of GROMACS or AMBER simulations as well). \r\n\r\nAt this point, I have in mind particularly the workflow for setting up protein+ligand simulations given \"well prepared\" structures of both protein + ligand. I think independently or together we've got fairly good workflows (or at least workflows which are under development) for fixing broken proteins/building the proteins we want, and for setting up ligands (including after docking them, if needed). To some degree I see the major hurdle as linking these parts of the process up (combining the protein+ligand and assigning final parameters). More generally we could think of the workflow as all-encompassing (protein setup + ligand placement/parameterization, etc.) but that's a larger problem.\r\n\r\nSome things I think we need to address in the short-term are:\r\n\r\n1. *What would this workflow do (in the short term)?* The thing I most immediately need is \"if I have a clean, prepared protein PDB X, and a clean, charged GAFF ligand Y (with frcmod and mol2 files), how should I combine and solvate these?\" AMBER's tleap is the normal way, but simply writing wrappers for tleap is starting to feel archaic. What immediately appeals to me is to use some toolkit (AMBER tleap or GROMACS tools) to get the protein and ligand into separate parameter files (tleap for the ligand) and then ParmEd to combine them. It doesn't handle solvation, however, so how should that be done? I can use gromacs solvation tools to do it, but again this feels archaic. I did notice that openmm has in app a modeller functionality which has `addSolvent` functionality, but I am new to this ecosystem so I'm not sure if that would be a good way to do it. Also - what if I want to solvate my protein+ligand in non-water (i.e. water+DMSO, or water+TFE, or...)? Or should we build on what we've already done with packmol for pure solvents/mixtures and just use packmol as a general tool for solvation? \r\n\r\n2. *What code base/object type?* Should we be working within ParmEd or OpenMM? If OpenMM, will we be able to get prepared systems out and into some other format if we need? If not, that will impact our user base. If ParmEd or other, can we get prepared systems INTO OpenMM if needed? Will that bypass xml format forcefield stuff? What are the implications of this?\r\n\r\n3. What longer-term needs do we have for this workflow and what's the game plan for addressing them? Specifically, there are the usual problems with missing residues/loops in proteins, protonation states of protein residues, etc. On the ligand side, we might also be interested in general strategies for generating starting placements of ligands when crystal structures aren't available (OEDocking toolkit?) etc. \r\n\r\nHere I'm hoping we'll at least be able to address 1 and 2. "},"comment":{"url":"https://api.github.com/repos/choderalab/yank/issues/comments/224436398","html_url":"https://github.com/choderalab/yank/issues/248#issuecomment-224436398","issue_url":"https://api.github.com/repos/choderalab/yank/issues/248","id":224436398,"user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"created_at":"2016-06-07T22:41:10Z","updated_at":"2016-06-07T22:41:10Z","body":"@andrrizzi has part of this done, but there are still things we plan to address."}}
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