choderalab/protons

Protons
=======

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Testbed for constant-pH methodologies using OpenMM.

## Manifest ##

`protons/`  - Python module implementing constant-pH methodologies in Python

```
   calibration.py        - Calibration engines
   cnstphgbforces.py     - CustomGBForces that exclude contributions from discharged protons
   ligutils.py           - Work in progress code for ligand parametrization.
   tests/                - Unit tests
```

`protons/examples/`

```
   explicit-solvent-example.py - explicit solvent NCMC example
   amber-example/        - example system set up with AmberTools constant-pH tools
   calibration-implicit/ - terminally-blocked amino acids parameterized for implicit solvent relative free energy calculations
   calibration-explicit/ - terminally-blocked amino acids parameterized for explicit solvent relative free energy calculations
```

`references/`           - some relevant literature references

## Dependencies ##

`protons` will eventually be made conda installable. The list of dependencies can be found [here](devtools/conda-recipe/meta.yaml).  


## Contributors / coauthors ##
* Bas Rustenburg <bas.rustenburg@choderalab.org>
* Gregory Ross <gregory.ross@choderalab.org>
* John D. Chodera <choderaj@mskcc.org>
* Patrick Grinaway <grinawap@mskcc.org>
* Jason Swails <jason.swails@gmail.com>
* Jason Wagoner <jawagoner@gmail.com>