Changelog¶
All notable changes to PRISM will be documented here.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
[2.0.0] - 2025-02¶
Added¶
- PMF Module: Complete umbrella sampling and WHAM analysis workflow
- Metropolis-Hastings optimized pulling direction selection
- Automated SMD, umbrella window setup, and WHAM analysis
- Binding free energy calculations with bootstrap error estimation
- REST2 Module: Replica Exchange with Solute Tempering 2
- Geometric temperature ladder generation
- Automatic hot region identification and topology scaling
- Multi-replica Hamiltonian exchange setup
- MM/PBSA Module: Binding energy calculations
- Single-frame and trajectory-based modes
- gmx_MMPBSA and AMBER MMPBSA.py backends
- Automatic GROMACS-to-AMBER topology conversion
- Gaussian RESP Charges: HF/6-31G* and DFT charge calculations
- Gaussian input file generation
- Two-stage RESP fitting
- Integration with GAFF/GAFF2 parameterization
- Batch Processing: High-throughput virtual screening support
- Interactive Visualization: HTML-based contact analysis
- Trajectory Processing: PBC artifact correction and format conversion
- Multi-Ligand Support: Handle multiple ligands in a single system
- Configuration System: YAML-based configuration files
Changed¶
- Improved protein preparation with enhanced metal ion handling
- Enhanced error messages with colored terminal output
- Optimized ligand parameterization speed
- Improved meeko dependency handling and protonation mode
Fixed¶
- OPLS-AA force field generation issues
- Box size calculation for large systems
- Ion concentration accuracy
- Trajectory analysis memory usage
Reporting Issues¶
Found a bug?
- Check if it's already reported: GitHub Issues
- Create new issue with:
- PRISM version (
prism.get_version()) - Python version
- Operating system
- Minimal example to reproduce
Contributing¶
For contributions, please open an issue or pull request on GitHub.
Last Updated: February 2025