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MobleyLab / benchmarksets

Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
BSD 3-Clause "New" or "Revised" License
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Provide bound-state starting structures for hosts #50

Open davidlmobley opened 7 years ago

davidlmobley commented 7 years ago

The CB7 and GDCC guest input files do not have coordinates which correspond to a bound state in the host.

Per Niel:

They are close [to bound], but clearly not a plausible bound state. Jane made these files, and I don't see a way to fix this without manually setting them up or extracting conformations from the equilibrated prmtop/rst7 files.

I now have a Jupyter notebook I've prepared for SAMPL6 which can dock guests to hosts, so we should be able to re-generate these files from compound isomeric SMILES strings. It'll just take me a bit of time to get to that.

davidlmobley commented 7 years ago

(If someone else wants to do it, and has an OEChem license, let me know and I'll just provide the notebook. We could actually put it on this repo and use it to re-generate all the guest structures if needed.)

davidlmobley commented 7 years ago

It's worth noting that this re-generation process would also fix any issues @nhenriksen noted with bond/atom types for carboxylates and others such as amides, as in this comment: https://github.com/MobleyLab/benchmarksets/pull/47#issuecomment-323459533

davidlmobley commented 7 years ago

@nhenriksen - in case you're interested in it, the Jupyter notebook for SAMPL6 is up here: https://github.com/MobleyLab/SAMPL6/blob/master/host_guest/GenerateInputs.ipynb

I could adapt it for these purposes (and probably will at some point).

jchodera commented 7 years ago

@andrrizzi: Did you generate these for our YANK simulations? If so, could that script be used more generally here?

davidlmobley commented 7 years ago

@jchodera - as I understand it he used a manual alignment procedure or something similar; I don't think anyone had a script for docking to these systems yet. I believe the one I just linked to above is the first one from our groups.