Merge pull request #44 from MobleyLab/mobley

Update readme to include fixes from PR 42

README.md

@@ -35,10 +35,10 @@ All three host-guest components of this challenge are now final and launched, th
 - **Release 0.1.1** (July 22, 2019, DOI [10.5281/zenodo.3346023](https://dx.doi.org/10.5281/zenodo.3346023)): Includes updated README files that should have been in release 0.1.
 - **Release 0.1.2** (Sept. 16, 2019, DOI [10.5281/zenodo.3432298](https://dx.doi.org/10.5281/zenodo.3432298)): Fixes protonation states for three "modified cyclodextrin" hosts which had accidentally been prepared (and drawn in ChemDraw) with charged groups present as neutral -- specifically terminal -NH3 groups were provided as -NH2. This affected MGLab19, 24 and 34. Also includes minor maintenance fixes -- listing final rather than tentative buffer conditions for GDCC case (just removing the "tentative" on the buffer identity, and correcting pH from 11.5 to 11.7); updates submission deadlines; fixes missing coordinates in TrimerTrip `g11`; fixing breakdown into residues in a couple modified cyclodextrin host PDB/mol2 files.
 - **Release 0.2** (Sept. 24, 2019, DOI [10.5281/zenodo.3459975](https://dx.doi.org/10.5281/zenodo.3459975)): Adds host-guest submission template files and instructions; makes more clear which compounds/cases are optional; makes clear that free energy predictions (and uncertainties) are required; enthalpies optional; adds links to [host-guest submission system](http://sampl-submission.us-west-1.elasticbeanstalk.com/submit/)
+- **Release 0.3** (Sept. 26, 2019): Corrected likely charges/protonation states for MGLab23 and MGLab24 in overview table and in jpg and PDF files. Updated corresponding coded and noncoded CDX files. Fixed a mixture of UNK and MGO residue names. Eliminates all instances of atom name HQ which should correspond to a carbon (which for some reason was instead named HX in some hosts, likely causing problems for some workflows). This has been mapped to atom name C9. Reconnects missing bonds in the PDB section of several models. See [PR 42](https://github.com/MobleyLab/SAMPL7/pull/42) for full details. Also removes outdated info in README.md and removes extra guest listed in TrimerTrip submission template.
 
 ### Changes not in a release
-- Remove outdated info in README.md
-- Remove extra guest listed in TrimerTrip submission template
+
 
 ## Challenge overview
 

host_guest/cyclodextrin_derivatives/README.md

@@ -34,6 +34,8 @@ Compounds exhibiting strange binding patterns have already been removed prior to
 
 Note that we have typically selected reasonable protonation states and conformers of the hosts and guests, but these may be controversial, uncertain, or change upon binding, so participants are encouraged to exercise care in selecting which states are modeled.
 
+(Please note that we made a significant update to the provided protonation states on Sept. 26, 2019, for version 0.3, as the originally provided protonation states were likely incorrect for certain hosts -- see [PR 42](https://github.com/MobleyLab/SAMPL7/pull/42) and the main README.md for more details).
+
 # What's here
 
 - Hosts: `host_files`: Folder containing beta cyclodextrin plus the eight other cyclodextrin derivative hosts, provided by Katy Kellett and Michael Gilson, initially only in PDB format with all protons present. The Chemdraw files are also provided. MOL2 and SDF files of the hosts were added on 7/18/19.