# gmx_MMPBSA

**Repository Path**: dhxia007/gmx_MMPBSA

## Basic Information

- **Project Name**: gmx_MMPBSA
- **Description**: 受体-配体（如蛋白质-药物小分子）GROMACS分子动力学轨迹结合自由能计算程序
- **Primary Language**: Python
- **License**: GPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2024-01-16
- **Last Updated**: 2024-01-19

## Categories & Tags

**Categories**: Uncategorized

**Tags**: 分子动力学, 结合自由能, GROMACS, cadd

## README

[![Python](https://img.shields.io/badge/Python-v3.x-blue)]()
[![Pypi](https://img.shields.io/pypi/v/gmx-MMPBSA)](https://pypi.org/project/gmx-MMPBSA/)
[![Downloads](https://pepy.tech/badge/gmx-mmpbsa)](https://pepy.tech/project/gmx-mmpbsa)
[![DOI](https://img.shields.io/badge/DOI-10.1021%2Facs.jctc.1c00645-blue)](https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645)

[![Help forum](https://img.shields.io/badge/Docs-Getting_Started-blue)](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/getting-started/)
[![Help forum](https://img.shields.io/badge/Help_forum-Google_group-blue)](https://groups.google.com/g/gmx_mmpbsa)
[![Issue tracking](https://img.shields.io/badge/Issue_tracking-GitHub-blue)](https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues)

[![Support](https://img.shields.io/badge/Support-JetBrains-brightgreen)](https://www.jetbrains.com/?from=gmx_MMPBSA)
[![Support](https://img.shields.io/badge/Support-Sourcery-orange)](https://sourcery.ai/invite/gndRrjlo)


# Welcome to gmx_MMPBSA!
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS 
files. It works with all GROMACS versions along with AmberTools >= 20.

**Please see the documentation [here](https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/getting-started)**

## Cite us

<a href="https://www.scimagojr.com/journalsearch.php?q=5100155074&amp;tip=sid&amp;exact=no" title="SCImago Journal 
&amp; Country Rank"><img border="0" align="right" src="https://www.scimagojr.com/journal_img.php?id=5100155074" 
alt="SCImago Journal &amp; Country Rank"  /></a>

Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A. and Moreno E. **gmx_MMPBSA: A New Tool to Perform 
End-State Free Energy Calculations with GROMACS**. _Journal of Chemical Theory and Computation_, 2021 17 (10), 6281-6291
https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645

Please also consider citing MMPBSA.py's paper:

Bill R. Miller, T. Dwight McGee, Jason M. Swails, Nadine Homeyer, Holger Gohlke, and Adrian E. Roitberg. **MMPBSA.py: 
An Efficient Program for End-State Free Energy Calculations**. _Journal of Chemical Theory and Computation_, 2012 8 
(9), 3314-3321. https://pubs.acs.org/doi/10.1021/ct300418h

Please, visit [Cite gmx_MMPBSA](cite_us.md) page for more information on how to cite gmx_MMPBSA and the programs/methods implemented in it.

---------------------------------------

Authors:
- [Mario Sergio Valdés Tresanco](https://www.researchgate.net/profile/Mario-Valdes-Tresanco-2), PhD Student. _University of Medellin, Colombia_
- [Mario Ernesto Valdés Tresanco](https://www.researchgate.net/profile/Mario-Valdes-Tresanco), PhD Student. _University of Calgary, Canada._
- [Pedro Alberto Valiente](https://www.researchgate.net/profile/Pedro-Valiente), PhD. _University of Toronto, Canada_
- [Ernesto Moreno Frías](https://www.researchgate.net/profile/Ernesto-Moreno-Frias), PhD. _University of Medellin, Colombia_

---------------------------------------

Acknowledgements:
- First of all, to Amber and GROMACS developers. Without their incredible and hard work, gmx_MMPBSA would not exist.
- Jason Swails (Amber developer and [ParmEd](https://github.com/ParmEd/ParmEd) principal developer) for his continuous support on ParmEd issues.
- Dr. Hymavathi Veeravarapu for helping with the [introductory video](https://www.youtube.com/watch?v=_2mYeffqFIo) for gmx_MMPBSA.
- To the Open Source license of the [JetBrains](https://www.jetbrains.com) programs.
- To the [Sourcery](https://sourcery.ai/invite/gndRrjlo) team for supporting us with the [Pro version](https://sourcery.ai/pro/).
- To all researchers that help improving gmx_MMPBSA with comments, feedback, and bug reports.

---------------------------------------