Welcome to s_mmpbsa Documentation

s_mmpbsa is an efficient tool for calculating biomolecular binding free energy, specifically designed for analyzing Gromacs trajectories using the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method.

Content Overview

• Introduction
  • Introduction to MM-PBSA Method
  • Why Choose s_mmpbsa?
  • s_mmpbsa’s Basic Workflow
  • Application Scenarios
  • Theoretical Innovations
  • License Information
  • Citing s_mmpbsa
• Installation
  • System Requirements
  • Software Dependencies
  • Installation Methods
  • Verifying Installation
  • Configuring s_mmpbsa
  • Frequently Asked Questions
  • Getting Help
• Quick Start
  • Starting s_mmpbsa
  • Basic Workflow
  • Loading Input Files
  • Setting Trajectory Parameters
  • Setting MM-PBSA Parameters
  • Executing Calculation
  • Analyzing Results
  • Using Analysis Mode
  • Example: Calculating Protein-Ligand Binding Energy
  • Usage Tips
  • Frequently Asked Questions
• Usage
  • Command Line Parameters
  • Interactive Command Line Interface
  • File Loading
  • Trajectory Parameter Setting
  • MM-PBSA Parameter Setting
  • Executing Calculation
  • Result Analysis
  • Using Analysis Mode
  • Alanine Scanning
  • Interpretation of Calculation Results
  • Notes
  • More Information
• API Documentation
  • Project Structure
  • Main Modules
  • main Module
  • mmpbsa Module
  • analysis Module
  • parse_tpr Module
  • parse_ndx Module
  • parse_xtc Module
  • pdb Module
  • pbsa Module
  • mm Module
  • utils Module
  • settings Module
  • Key Data Structures
  • Using s_mmpbsa as a Library
  • Extending s_mmpbsa
  • Contribution Guidelines
  • More Information
• Frequently Asked Questions
  • Installation Issues
  • Usage Issues
  • Technical Issues
  • Result Analysis Issues
  • Other Issues
  • More Information

Introduction

s_mmpbsa provides a user-friendly interface (similar to Multiwfn) for calculating binding free energy from Gromacs trajectories. Compared to other similar tools, it offers advantages such as easy installation, efficient operation, cross-platform compatibility, and supports advanced features like charge screening effects and conformational entropy calculation.

Main Features

• MD Simulation Binding Energy Calculation: Calculate binding free energy between biomolecules from molecular dynamics simulation results

• Molecular Docking Result Rescoring: Provide more accurate binding energy predictions for molecular docking results

• Protein-Ligand Complex Alanine Scanning: Analyze the contribution of key residues in proteins to binding

Features

• Open source and free, under the LGPL license

• Minimal environment dependencies, only requiring Gromacs on Linux systems; Python environment needed for plotting functionality

• Developed in Rust language for excellent performance

• Interactive operation, no need to write parameter files

• Considers charge screening effects, as described in literature [J. Chem. Inf. Model. 2021, 61, 2454]

• Considers conformational entropy, as described in literature [J. Chem. Phys. 2017, 146, 124124]

• Can store analysis results for further reproducible analysis

Getting Started

Please refer to the Installation chapter to install s_mmpbsa, and then check the Quick Start chapter to learn the basic usage流程.

For detailed usage instructions, please refer to the Usage chapter, which contains usage methods and examples of various functions.

Getting Help

If you encounter any problems during use or have any suggestions for improvement, please contact the developer or join the QQ group:

• Developer: Dr. Jiaxing Zhang (zhangjiaxing7137@tju.edu.cn, Tianjin University)

• QQ Group: 864191465

Citation

If you use s_mmpbsa in your research work, please cite it in the following format:

Jiaxing Zhang, s_mmpbsa, Version [your version], https://github.com/supernova4869/s_mmpbsa (accessed on yy-mm-dd)

Note

When a detailed paper on s_mmpbsa is published, please cite the corresponding paper instead of this webpage.

Index and Tables

• Index

• Module Index

• Search Page