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All Projects → choderalab → protons

choderalab / protons

Licence: MIT license
OpenMM testbed for constant-pH methodologies.

Programming Languages

python
139335 projects - #7 most used programming language

Labels

simulationopenmmconstant-phprotonph-methodologies

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Protons

Build Status Documentation Status codecov Code Climate

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.

Contributors / coauthors

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