{"repo":"AIB001/PRISM","free":true,"listed":false,"github":"https://github.com/AIB001/PRISM","clone":"git clone https://github.com/AIB001/PRISM.git","description":"PRISM (Protein Receptor Interaction Simulation Modeler) is a comprehensive tool for building protein-ligand systems for molecular simulations, including MD, PMF, REST2, etc. in GROMACS, developed by ZJUIQB. It supports multiple force fields for ligands including GAFF , OpenFF, CGENFF, Opls-AA, etc. MCP server is provided for AI-Agent","language":"Python","stars":30,"topics":[],"license":null,"category":"mcp-servers","readme_excerpt":"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","default_branch":null,"files":null,"tree":[],"storefront":"/r/AIB001","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/AIB001/PRISM/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}