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samplchallenges / SAMPL6

Challenge inputs, details, and results for the SAMPL6 series of challenges
https://samplchallenges.github.io
MIT License
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Update microstates lists and microstate definition of pKa challenge #28

Closed MehtapIsik closed 6 years ago

MehtapIsik commented 6 years ago

Updates for v1.5 of SAMPL6 repository for pKa challenge:

  1. Add working definition for pKa microstate: All geometric isomers and resonance structure pairs that have the same total charge and the same number of hydrogens bound to equivalent heavy atoms are related to the same microstate.
  2. Add a comment that only E-isomer of SM20 must be modeled. I did the experiments with pure E-isomer.
  3. Deprecated replicate microstates (mostly related to geometric isomers)
  4. Add back SM21_micro020 microstate which was deprecated by mistake. Bas identified it through Epik predictions.
  5. Add lists of suggested physical microstate pairs (microstates pairs that interconvert by one deprotonation event)
  6. Adding a canonical SMILES column in addition to canonical isomeric SMILES to SMXX_microstates.csv files for easier matching of predicted microstates to microstate IDs.

@davidlmobley @bannanc Could you please review and merge?

davidlmobley commented 6 years ago

Caitlin says she will be able to review soon.

MehtapIsik commented 6 years ago

OK. I'll wait for her feedback as much as I can today (~4 hours) before merging and sending the announcement email.

bannanc commented 6 years ago

@MehtapIsik This looks good to me. Are the pairs all in the same direction, that is would they all results in either a +1 or -1 charge difference as discussed in the e-mail discussion with Stefan? Assuming that is the case, I think this is ready to merge.

MehtapIsik commented 6 years ago

Yes, I corrected the order of microstate pairs. The current order is deprotonation: ID1, ID2 HA, A