Provide bound-state starting structures for hosts

[davidlmobley]

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]

(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]

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: #47 (comment)

[davidlmobley]

@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]

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

[davidlmobley]

@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.