Protons: Protonation states and tautomers for OpenMM

Caution

This is module is undergoing heavy development. None of the API calls are final. This software is provided without any guarantees of correctness, you will likely encounter bugs.

If you are interested in this code, please wait for the official release to use it. In the mean time, to stay informed of development progress you are encouraged to:

• Follow this feed for updates on releases.
• Check out the github repository .

Table of contents

• 1. Introduction
• 2. Feature Roadmap
  • 2.1. Development notes
• 3. Installing Protons
  • 3.1. Install using conda
  • 3.2. Install using setup.py
  • 3.3. Requirements
  • 3.4. Testing your installation
• 4. Preparing systems for constant-pH simulation
  • 4.1. Obtaining and using Ambertools
  • 4.2. Fixing residue names and atoms
  • 4.3. Writing out coordinate and parameter files using Leap
  • 4.4. Including ligands in your system
  • 4.5. Generating parameters for amino acid protonation states
• 5. Running a constant-pH MD simulation
  • 5.1. Setting up the AmberProtonDrive class
  • 5.2. Solvent reference state calibrations
  • 5.3. Running the simulation
  • 5.4. Tracking the simulation
  • 5.5. Basic example
• 6. Advanced calibration options
• 7. The ligutils submodule
  • 7.1. Treating small molecules
• 8. API documentation
  • 8.1. The protons module
• 9. References

Indices and tables

• Index
• Module Index
• Search Page