Testbed for constant-pH methodologies using OpenMM.
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
protons will eventually be made conda installable. The list of dependencies can be found here.
- 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