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PRISM Documentation

Overview

Getting Started¶

PRISM automates the setup of protein-ligand molecular dynamics systems for GROMACS.

Quick Start

git clone https://github.com/AIB001/PRISM.git && cd PRISM
pip install -e .
prism protein.pdb ligand.mol2 -o my_system

Choose Your Path¶

Installation

Install GROMACS, Python dependencies, and PRISM itself
Quick Start

Build your first protein-ligand system in under 5 minutes

Prerequisites¶

Before you begin, ensure you have:

Python 3.8+ installed (3.10 recommended)
GROMACS 2024.3+ installed and sourced
A protein PDB file and a ligand MOL2/SDF file

Learning Path¶

graph LR
    A[Installation] --> B[Quick Start]
    B --> C[User Guide]
    C --> D[Tutorials]
    D --> E[Advanced Topics]

For Beginners¶

New to PRISM?

Follow the Installation guide
Run through the Quick Start with your own files
Read the Basic Tutorial for a step-by-step walkthrough

For Experienced Users¶

Coming from other MD tools?

Jump to Force Fields Guide for supported options
See PMF Calculations for binding free energy
Browse the API Reference for scripting

Troubleshooting¶

Having issues? Check these resources:

What's Next¶