Comments (3)
Related to (but maybe more specific than) #49 and #1.
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Agreed, yes, we should do this.
I think there is a tool which perhaps could convert, I believe pandoc
?
Otherwise maybe CB7 is within @nhenriksen 's interests; GDCC would probably fall to me.
from benchmarksets.
I think you are right, although there are differences between the manuscript table and the ones in the READMEs. I understand this may be because you (?) did not want to bias the calculations by suggesting a particular charge state (I think...). In any case, I appreciate the READMEs in the CD set because the charge states and SMILES strings listed there conform exactly to what I see in the files (at least so far), and I can use that as a sanity check or additional filter while doing the force field conversions. Anyway, this is not a sticking point for me, just an observation!
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Related Issues (20)
- Add README.md for host-guest inputs; add additional info
- Update text to reflect host-guest sets added in #22 HOT 1
- CD mol2 files coordinates starting in the binding pocket HOT 20
- Add additional supplementary data, perhaps in markdown files? HOT 5
- Get CD benchmarks in? HOT 3
- Provide suitable README files for CB7, GDCC benchmarks
- Provide bound-state starting structures for hosts HOT 5
- Deposit calculated values for provided files when available HOT 5
- Should we use table titles and not numbers in markdown files? HOT 6
- Provide compound ID for all files HOT 5
- Parmed bug affecting cyclodextrin files HOT 6
- Update README.md to reflect how to cite (once discussion is final) HOT 4
- Mixed 1-4 scaling? HOT 2
- Typo in reference for Lysozyme L99A/M102Q - catechol experimental value? HOT 3
- Errors using cyclic host `mol2` files with non-unique atom names HOT 11
- The SDF files for charged compounds aren't listing the formal charges of the atoms HOT 2
- PDB files for BRD4 parameterized systems are missing CONECT records HOT 2
- Include additional data, references
- gdcc-set2 and CB experimental Delta H is missing HOT 4
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