AMMo

AMMo (Allostery in Markov Models) is a collection of a python library, command line scripts and tools, for assessing allosteric modulators. The main use for easier Markov State Model building and comparison, using steered MD simulations to explore a larger conformational space. Depending on how much customization is desired, there are 3 levels of tools available:

The highest level is the set of command line tools that create and run an AMMo project. The lowest level is the ammo python library, with some default functions to run and analyse MD simulations (if even more customization is needed, BioSimSpace is recommended to set up own simulations). The command line scrips simply run the functions available in the python library from the command line, allowing for easier execution and job scheduling.

Examples

In-depth explanations on how to use the python library, the command line scripts, and the AMMo project are available in the ammo_basic of examples folder. Example folder also includes two case studies on applying AMMo to Protein Tyrosine Phosphatase 1B (PTP1B) and Exchange Proteins directly Activated by cAMP (EPACs).

Installation

To use ammo, clone this repository and run python setup.py.

The Python interpreter used to run AMMo commands (default: /usr/bin/python3) and the location of allostery projects (default: ~/Documents) can be set by adding the arguments --interpreter and --location when running python python setup.py.

These settings can also be modified in the configuration file after setup.

Requirements

• a python evnironment containing:
  • BioSimSpace
  • pytraj¹
• AMBER¹
• GROMACS

Footnotes

1. If AMBER is compiled with pytraj compatible with the BioSimSpace environment, a separate installation of pytraj is not needed. If AMBER is compiled with pytraj that is not compatible with the BioSimSpace environment, it needs to be removed from PYTHONPATH and a separate pytraj installed in the environment. ↩ ↩²