Automated Martini 3 Coarse-Graining Framework

A Python-based framework for automatically generating Martini 3 coarse-grained models directly from SMILES strings.
This tool is designed to transform the complex, manual process of creating coarse-grained topologies into a fast, systematic, and reproducible workflow.

---

Overview

The Martini 3 force field is a powerful tool for large-scale molecular simulations, but its use depends on a crucial mapping step where atoms are grouped into coarse-grained beads.
This has traditionally been a slow, manual process requiring significant chemical expertise.

This framework automates that entire process. It uses a sophisticated, rule-based algorithm to intelligently partition a molecule and assign the correct bead types, producing simulation-ready files without any manual intervention.

---

Key Features

• Fully Automated: Go from a SMILES string to simulation-ready GROMACS files in a single step.
• Rule-Based and Extensible: Uses a detailed, internal dictionary of chemical fragments that can be expanded to map new structures.
• Hierarchical Mapping: Employs a "most-constrained-first" strategy, mapping rigid ring systems before flexible chains to ensure a robust and chemically sound model.
• Standardized Outputs: Generates GROMACS-compatible .gro (coordinate) and .itp (topology) files.

---

Installation

This project relies on RDKit for processing chemical structures.
The recommended way to set up the environment is by using Anaconda.

If you don’t already have Anaconda installed, you can download it here:
Install Anaconda

---

Setup Steps

# Clone the repository
git clone https://github.com/eliobaby/Martini_3.git
cd Martini_3

# Create a new Conda environment
conda create -n martini_mapper python=3.9

# Activate the environment
conda activate martini_mapper

# Install RDKit
conda install -c conda-forge rdkit

## Usage

The script is run interactively from the command line.

```bash
python main.py

You will be prompted for:

• Name: The name of your molecule.
• SMILES: The SMILES string representation of your molecule.

Example Session

$ python main.py
Name: Aspirin
SMILES: CC(=O)OC1=CC=CC=C1C(=O)O

---

Output Files

After running, the script will generate three files in the same directory:

• <MOLECULE_NAME>.gro: A GROMACS coordinate file containing the 3D positions of each coarse-grained bead.
• <MOLECULE_NAME>.itp: A GROMACS topology file that defines the bead types, bonds, and other parameters for the simulation.
• <MOLECULE_NAME>.txt: A detailed summary file showing how each atom was mapped, which bead it belongs to, and how the beads are connected. This file is very useful for debugging and validating the mapping.

---

Limitations

This framework is under active development. The current version has the following limitations:

• The internal mapping dictionary has been primarily developed using molecules containing Carbon, Oxygen, and Nitrogen.
• Support for other elements like Sulfur, Phosphorus, and halogens is still experimental.
• The algorithm may fail on molecules containing highly unusual or complex chemical fragments that are not yet present in the dictionary.

---

Future Directions

• Expand the Dictionary: Systematically test the framework on more diverse chemical datasets to add new rules and increase the mapping success rate.
• Integrate Machine Learning: Develop a machine learning model to assist with the tuning of bead parameters, which is currently a manual process.

---

Citation

If you use this work in your research, please cite our upcoming paper:

---

License