Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods
☆21Oct 31, 2019Updated 6 years ago
Alternatives and similar repositories for AmberUtils
Users that are interested in AmberUtils are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Quantum Mechanical Bespoke Force Field Derivation Toolkit☆15Jun 23, 2020Updated 6 years ago
- Gromacs molecular dynamics simulation analysis scripts☆10Apr 5, 2022Updated 4 years ago
- Real time monitoring and visualization of Amber MD simulations☆16Feb 6, 2020Updated 6 years ago
- Superseded by FabSim3.☆14Jun 11, 2019Updated 7 years ago
- Collected scripts for Pymol☆10Mar 18, 2015Updated 11 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Utilities for interacting with PubChem☆18Feb 11, 2015Updated 11 years ago
- Protein preparation for MD, made faster and easier !☆15Dec 18, 2023Updated 2 years ago
- Analysis of non-covalent interactions in MD trajectories☆72Jan 3, 2025Updated last year
- pKa estimates for proteins using an ensemble approach☆31Jul 24, 2026Updated 3 months ago
- ☆20Nov 10, 2021Updated 4 years ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆35Aug 8, 2026Updated 2 months ago
- ☆35Aug 28, 2026Updated 2 months ago
- Advanced toolkit for binding free energy calculations☆36Sep 2, 2025Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆44Apr 27, 2026Updated 6 months ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Paper for release☆11Sep 24, 2021Updated 5 years ago
- (Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina☆76Aug 3, 2023Updated 3 years ago
- Models trained on the SPICE dataset☆10Sep 23, 2022Updated 4 years ago
- Transferable Double Exponential non-bonded potential for condensed phase simulations of small molecules☆26Jul 17, 2026Updated 3 months ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 6 years ago
- Source code for the BUDE Alanine Scan web application.☆15May 27, 2025Updated last year
- SAnDReS: Statistical Analysis of Docking Results and Scoring functions (Version 2.0)☆21Updated this week
- Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations☆32May 6, 2024Updated 2 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆183Jul 28, 2026Updated 3 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Gaussian accelerated Molecular Dynamics in OpenMM☆10Jan 7, 2025Updated last year
- Statistical models for biomolecular dynamics☆45May 8, 2025Updated last year
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆69Apr 16, 2021Updated 5 years ago
- A collection of useful tutorials for Protein Science☆18Jun 29, 2015Updated 11 years ago
- a quick primer on making prettier (and more impactful) plots☆14Sep 27, 2015Updated 11 years ago
- An experimental package for deep learning for molecular docking☆22Mar 21, 2020Updated 6 years ago
- ☆32Oct 19, 2023Updated 3 years ago
- OpenMM plugin to interface with PLUMED☆82Aug 31, 2026Updated last month
- Mirror of pDynamo computational chemistry software, which does not currently use a public version control repository☆10Feb 23, 2017Updated 9 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Tautomer ratios in solution☆28Sep 20, 2021Updated 5 years ago
- Membrane protein builder and parameterizer☆19Sep 1, 2024Updated 2 years ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆30Jan 23, 2024Updated 2 years ago
- The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.☆13Mar 31, 2026Updated 6 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- Interactive plotting of data annotated with molecule structures.☆12Nov 30, 2023Updated 2 years ago
- ☆12May 7, 2026Updated 5 months ago