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
- John D. Chodera [email protected]
- Patrick Grinaway [email protected]
- Jason Swails [email protected]
- Jason Wagoner [email protected]