gmx-MMPBSA

v1.6.4

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files For more information about how to use this package see README

Latest version published 2 months ago

License: GPL-3.0

PyPI

GitHub

Package Health Score

69 / 100

security
Security review needed
popularity
Limited
maintenance
Healthy
community
Active

Popularity

Limited

GitHub Stars: 230
Forks: 67
Contributors: 5

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package gmx-MMPBSA, we found that it has been starred 230 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Nov 4, 2024
Direct Vulnerabilities: 0
C
0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 1
H
0
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

GPL-3.0

Non-Permissive License

We noticed that this project uses a license which requires less permissive conditions such as disclosing the source code, stating changes or redistributing the source under the same license. It is advised to further consult the license terms before use.

Security Policy

We found a way for you to contribute to the project! Looks like gmx-MMPBSA is missing a security policy.

You can connect your project's repository to Snyk to stay up to date on security alerts and receive automatic fix pull requests.

Keep your project free of vulnerabilities with Snyk

Maintenance

Healthy

Commit Frequency

Open Issues: 40
Open PR: 0
Last Release: 2 months ago
Last Commit: 25 days ago

Further analysis of the maintenance status of gmx-MMPBSA based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that gmx-MMPBSA demonstrates a positive version release cadence with at least one new version released in the past 3 months.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: Yes
Contributors: 5
Funding: Yes

This project has seen only 10 or less contributors.

Embed Package Health Score Badge

Keep your project healthy

Check your requirements.txt

Ensure all the packages you're using are healthy and well-maintained

Snyk Vulnerability Scanner

Get health score & security insights directly in your IDE

Package

Python Versions Compatibility: Unspecified

Age: 4 years
Latest Release: 2 months ago
Dependencies: 1 Direct / 17 Total
Versions: 26
Maintainers: 0
Wheels: OS Independent

Readme

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

Cite us

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 page for more information on how to cite gmx_MMPBSA and the programs/methods implemented in it.

Authors:

Mario Sergio Valdés Tresanco, PhD Student. University of Medellin, Colombia
Mario Ernesto Valdés Tresanco, PhD Student. University of Calgary, Canada.
Pedro Alberto Valiente, PhD. University of Toronto, Canada
Ernesto Moreno Frías, 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 principal developer) for his continuous support on ParmEd issues.
Dr. Hymavathi Veeravarapu for helping with the introductory video for gmx_MMPBSA.
To the Open Source license of the JetBrains programs.
To the Sourcery team for supporting us with the Pro version.
To all researchers that help improving gmx_MMPBSA with comments, feedback, and bug reports.

gmx-MMPBSA dependencies

tqdm

FAQs

What is gmx-MMPBSA?

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS ... Visit Snyk Advisor to see a full health score report for gmx-MMPBSA, including popularity, security, maintenance & community analysis.

Is gmx-MMPBSA popular?

The python package gmx-MMPBSA receives a total of 752 weekly downloads. As such, gmx-MMPBSA popularity was classified as limited. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is gmx-MMPBSA well maintained?

We found that gmx-MMPBSA demonstrated a healthy version release cadence and project activity. It has a community of 5 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is gmx-MMPBSA safe to use?

While scanning the latest version of gmx-MMPBSA, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 21 December-2024, at 20:56 (UTC).

Build a secure application checklist

Select a recommended open source package

Minimize your risk by selecting secure & well maintained open source packages

DONE

Scan your app for vulnerabilities

Scan your application to find vulnerabilities in your: source code, open source dependencies, containers and configuration files

SCAN NOW

Fix identified vulnerabilities

Easily fix your code by leveraging automatically generated PRs

AUTO FIX

Monitor for new issues

New vulnerabilities are discovered every day. Get notified if your application is affected

MONITOR APP