MSM_PELE - MSM Free Energy Calculation Algorithm

MSM PELE is a Python library with the aim to calculate absolute free energies through MSM analysis over paralel monte carlo simulations. Currently, MSM PELE is build on top of of next softwares:

• Protein Energy Landscape Exploration Software

• Adaptive Sampling Simulation to boost Performance

• Markov State Model Analysis

Technical Features:

• Code is implemented in Python (supports 2.7)

• Runs on Linux (64 bits), Windows or MAC (64 bits).

• OpenmMP&MPI Implementation

• Schrodinger (2016/17/18) is needed.

MSM analysis over a potential energy surface of a ligand-protein complex

Installation

• Installation
  • Third Parties Requirements
  • Conda(Recommended)
  • Pypi
  • Source Code
  • Update latest changes from Github Code (once already installed)

Tests

• Production Test
  • Run production test

Tutorial

• Tutorial
  • Launch the job
  • Analise the exit path
  • Analise the MC exploration
  • Analise the MSM

Documentation

• Parameters
  • Required Paramaters:
  • Output Parameters
  • Restart Parameters
  • Input Preparation Parameters
    • receptor
    • ligand
  • Exit Simulation Parameters
  • Exit simulation clustering Parameters
  • Box Parameters
  • Exploration Parameters
    • metrics
    • waters
    • protocol
  • MSM Analysis

Benchmark

• Benchmark
  • Urokinase
  • Progesterone Receptor
  • ERK2
  • COMT
  • Plami
  • EPHB

Changelog

• Changelog
  • 2.1 - 28-10-2019
  • 2.0 - 21-02-2019
  • 1.1.0 - 02-10-2018
  • 1.0.3 - 4-07-2018
  • 1.0.2 - 4-05-2018
  • 1.0.1 - 3-16-2018

Support

• Support

Indices and tables

• Search Page