PRISM - Protein Receptor Interaction Simulation Modeler

PRISM is a comprehensive tool for building protein-ligand systems for molecular dynamics simulations in GROMACS. It supports multiple force fields for ligands including GAFF, GAFF2, OpenFF, CGenFF, OPLS-AA, and SwissParam (MMFF/MATCH/Hybrid).

Features

• Multiple Force Field Support
  • GAFF/GAFF2 via AmberTools
  • OpenFF via openff-toolkit
  • CGenFF (CHARMM General Force Field) via web download
  • OPLS-AA via LigParGen server
  • SwissParam (MMFF/MATCH/Hybrid) via SwissParam server
• Automatic System Building: Complete workflow from PDB/MOL2/SDF to simulation-ready files
• Flexible Configuration: YAML-based configuration for easy customization
• Smart File Processing: Handles various input formats with automatic conversion
• Position Restraints: Automatic generation for equilibration protocols
• Complete MDP Files: Pre-configured protocols for minimization, equilibration, and production
• Metal Ion Support: Intelligent recognition and handling of metal ions (Zn, Ca, Mg, Fe, etc.) with distance-based filtering
• Advanced Protein Cleaning: Smart removal of heteroatoms and crystallization artifacts while preserving structural metals
• Protonation State Prediction: Optional pKa-based protonation for ionizable residues with PROPKA (HIS/ASP/GLU/LYS/CYS/TYR)
• Protonation States: Support for special residue protonation states (CYM, HID, HIE, HIP, CYX, LYN, ASH, GLH)
• CADD-Agent

Installation

Prerequisites

1. GROMACS (required)

   # Ubuntu/Debian, CUDA-toolkit is needed, Dependence installation
   nvcc --version # For check
   sudo apt-get install gcc
   sudo apt-get install g++
   sudo apt-get install cmake
   
   # Download GROMACS Package
   wget https://ftp.gromacs.org/gromacs/gromacs-2025.1.tar.gz
   tar xfz gromacs-2025.1.tar.gz
   
   # Prepare to build GROMACS with cmake
   cd gromacs-2025.1
   mkdir build
   cd build
   
   # Installation
   cmake .. -DGMX_MPI=ON \
   -DGMX_BUILD_OWN_FFTW=ON \
   -DGMX_GPU=CUDA \
   -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
   -DCUDA_INCLUDE_DIRS=/usr/local/cuda/include \
   -DCUDA_CUDART_LIBRARY=/usr/local/cuda/lib64 \
   -DCMAKE_INSTALL_PREFIX=~/gromacs-2025.1
   
   make -j${nproc}
   make check # Optional but recommended
   sudo make install
   source /mnt/data/zf/gromacs-2024.3/bin/GMXRC
   
   # install bioconda
   conda install -c bioconda
   

2. Python 3.10 with required packages:

   # create environment 
   conda create -n prism python=3.10
   conda activate prism
   

3. PDBFixer and pyyaml (required)

   conda install -c conda-forge pdbfixer numpy scipy
   pip install pyyaml
   

Optional Dependencies

For Protonation State Prediction (optional):

# PROPKA for pKa-based protonation prediction (optional)
conda install -c conda-forge propka
# or
pip install propka>=3.4.0

# Or install with PRISM protonation extras
pip install -e .[protonation]

Force Field Specific Dependencies

For GAFF/GAFF2 Support:

# AmberTools (required)
conda install conda-forge::ambertools
# ACPYPE (required)
pip install acpype
# Optional but recommended
conda install -c conda-forge rdkit

For OpenFF Support:

# OpenFF toolkit and dependencies
conda install -c conda-forge openff-toolkit openff-interchange

# RDKit (required for SDF handling)
conda install -c conda-forge rdkit

# OpenBabel (Optional but Recommended)
conda install conda-forge::openbabel

For CGenFF Support:

CGenFF requires downloading force field files from the web server:

1. Visit https://cgenff.com/
2. Upload your ligand structure (MOL2/SDF)
3. Download the generated files (PDB and TOP f

... View full README on GitHub