PRISM은 GROMACS의 분자 역학 시뮬레이션을위한 단백질 리간드 시스템을 구축하기위한 종합 도구입니다. 그것은 GAFF, GAFF2, OpenFF, CGenFF, OPLS-AA 및 SwissParam (MMFF / MATCH / Hybrid)를 포함한 리간드의 여러 강제 필드를 지원합니다.

특징

• Multiple Force Field 지원
• **GAFF/GAFF2 ** AmberTools를 통해
• OpenFF 를 통해 openff-toolkit
• CGenFF (CHARMM General Force Field) 웹 다운로드
• ** OPLS-AA** LigParGen 서버를 통해
• SwissParam (MMFF/MATCH/Hybrid) 스위스파람 서버를 통해 -Automatic System Building: PDB/MOL2/SDF에서 시뮬레이션 읽기 파일로 작업 완료 -Flexible Configuration: 쉬운 사용자 정의를 위한 YAML 기반 구성
• Smart File Processing: 자동 변환과 다양한 입력 형식을 처리
• ** 중재 **: Equilibration 의정서를 위한 자동적인 발생 -Complete MDP Files: 최소화, equilibration 및 생산을위한 사전 구성 프로토콜
• ** 금속 이온 지원 ** : 거리 기반 필터링과 금속 이온 (Zn, Ca, Mg, Fe 등)의 지능형 인식 및 취급

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 ~/gromacs-2025.1/bin/GMXRC   # match CMAKE_INSTALL_PREFIX above
   
   # 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