<commit_before># SAMPL6 host-guest files


## Manifest
- `Gibb_SAMPL6_guests.cdxml`: ChemDraw file provided by <NAME> Aug. 18, 2017
- `Gibb_SAMPL6_guests.smi`: Isomeric SMILES format file for the same guests, created by <NAME> Aug. 18, 2017. Format is "smiles name" on each line. Created by using selecting each structure in ChemDraw, choosing "copy as -> smiles", and then pasting into (a) Picto to check, and (b) this text file to save. Names typed by hand.
- `Isaacs_SAMPL6_guests.cdx`: ChemDraw file provided by <NAME> Aug. 18, 2017
- `Isaacs_SAMPL6_guests.smi`: Isomeric SMILES format file for the same guests, created by <NAME> Aug. 18, 2017; the SMILES for palonosetron was updated 8/22/17 after careful treatment of stereochemistry by Isaacs and Mobley. Format is "smiles name" on each line. Created by selecting each structure in ChemDraw, choosing "copy as -> smiles", and then pasting into (a) Picto to check, and (b) this text file to save. Names typed by hand. NOTE: Salts were not copied, only the guest molecules (tartrate and oxalate have been verified not to bind). N2: Gallamine triethiodate SMILES was taken from Wikipedia and manually verified to match the intended structure. N3: Chirality of bicyclic ring system bridgehead carbon did not propagate properly from ChemDraw to SMILES; manually re-added in MarvinSketch and verified using Picto before pasting SMILES here.
- `OctaAcidsAndGuests/`: Directory containing octa acid (OA and TEMOA) input structures and guest structure files
- `CB8AndGuests/`: Directory containing CB8 input structure and guest structure files
- `GenerateInputs.ipynb`: Jupyter notebook using the OpenEye toolkits to generate molecule structure files from the other inputs noted above
- `SAMPLing/`: Equilibrated system files for the SAMPLing challenge. These include all host-guest systems in the SAMPL6 challenge with the exception of oxalipatin (CB8-G13). Files are available in Amber (`prmtop`/`rst7`), Gromacs (`top`/`gro`), OpenMM (`xml`) and PDB formats. See below for the setup protocol.

## SAMPLing files preparation

All the host-guest system files in the `SAMPLing/` directory were prepared using the protocol below.
- Protonation states and initial starting configurations were taken as given by the original `mol2` files in the `OctaAcidsAndGuests/` and `CB8AndGuests/` directories.
- Hosts and guests were both parametrized with GAFF v1.8 and antechamber. AM1-BCC charges were generated using OpenEye's QUACPAC toolkit through `openmoltools 0.8.1`.
- The host-guest complex were solvated in a 12A buffer of TIP3P water molecules using tleap.
- The systems' net charge was neutralized with Na+ and Cl- ions. More ions were added to reach the ionic strength of 10mM for OA/TEMOA systems and 25mM for CB8.
- The system was minimized with the L-BFGS optimization algorithm and equilibrated by running 1ns of Langevin dynamics (BAOAB splitting, 1fs time step) at 298.15K with a Monte Carlo barostat set at 1atm using `OpenMM 7.1.1`. PME was used for long-range electrostatic interactions with a cutoff of 10A. VdW interactions used the same 10A cutoff and a switching distance of 9A.<commit_msg>Mention complex and solvent files in SAMPLing README<commit_after># SAMPL6 host-guest files


## Manifest
- `Gibb_SAMPL6_guests.cdxml`: ChemDraw file provided by <NAME> Aug. 18, 2017
- `Gibb_SAMPL6_guests.smi`: Isomeric SMILES format file for the same guests, created by <NAME> Aug. 18, 2017. Format is "smiles name" on each line. Created by using selecting each structure in ChemDraw, choosing "copy as -> smiles", and then pasting into (a) Picto to check, and (b) this text file to save. Names typed by hand.
- `Isaacs_SAMPL6_guests.cdx`: ChemDraw file provided by <NAME> Aug. 18, 2017
- `Isaacs_SAMPL6_guests.smi`: Isomeric SMILES format file for the same guests, created by <NAME> Aug. 18, 2017; the SMILES for palonosetron was updated 8/22/17 after careful treatment of stereochemistry by Isaacs and Mobley. Format is "smiles name" on each line. Created by selecting each structure in ChemDraw, choosing "copy as -> smiles", and then pasting into (a) Picto to check, and (b) this text file to save. Names typed by hand. NOTE: Salts were not copied, only the guest molecules (tartrate and oxalate have been verified not to bind). N2: Gallamine triethiodate SMILES was taken from Wikipedia and manually verified to match the intended structure. N3: Chirality of bicyclic ring system bridgehead carbon did not propagate properly from ChemDraw to SMILES; manually re-added in MarvinSketch and verified using Picto before pasting SMILES here.
- `OctaAcidsAndGuests/`: Directory containing octa acid (OA and TEMOA) input structures and guest structure files
- `CB8AndGuests/`: Directory containing CB8 input structure and guest structure files
- `GenerateInputs.ipynb`: Jupyter notebook using the OpenEye toolkits to generate molecule structure files from the other inputs noted above
- `SAMPLing/`: Equilibrated system files for the SAMPLing challenge. These include all host-guest systems in the SAMPL6 challenge with the exception of oxalipatin (CB8-G13). Files are available in Amber (`prmtop`/`rst7`), Gromacs (`top`/`gro`), OpenMM (`xml`) and PDB formats. Solvated system files are available both for the host-guest complex (e.g. `complex.pdb`) and the guest alone (e.g. `solvent.pdb`). See below for the setup protocol.

## SAMPLing files preparation

All the host-guest system files in the `SAMPLing/` directory were prepared using the protocol below.
- Protonation states and initial starting configurations were taken as given by the original `mol2` files in the `OctaAcidsAndGuests/` and `CB8AndGuests/` directories.
- Hosts and guests were both parametrized with GAFF v1.8 and antechamber. AM1-BCC charges were generated using OpenEye's QUACPAC toolkit through `openmoltools 0.8.1`.
- The systems were solvated in a 12A buffer of TIP3P water molecules using tleap.
- The systems' net charge was neutralized with Na+ and Cl- ions. More ions were added to reach the ionic strength of 10mM for OA/TEMOA systems and 25mM for CB8.
- The system was minimized with the L-BFGS optimization algorithm and equilibrated by running 1ns of Langevin dynamics (BAOAB splitting, 1fs time step) at 298.15K with a Monte Carlo barostat set at 1atm using `OpenMM 7.1.1`. PME was used for long-range electrostatic interactions with a cutoff of 10A. VdW interactions used the same 10A cutoff and a switching distance of 9A.
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