Use This MCP server To

Enable AI to control molecular visualization tools like PyMOL Integrate ChimeraX for interactive molecule modeling with AI Use Gromacs copilot for AI-assisted molecular dynamics simulations Automate molecule structure analysis via AI-driven tool commands Facilitate prompt-based molecule modeling workflows with Claude AI Connect multiple molecule science tools for unified AI interaction Streamline scientific research by combining AI and molecular software

README

Molecule-MCP

Molecule-MCP: A model-context-protocol server for molecules. Molecule-MCP connects molecule science releated tools to Claude AI through the Model Context Protocol (MCP), allowing Claude to directly interact with and control these tools and act as a co-scientist. This integration enables prompt assisted molecule modeling.

Installation

⚠️ Note: Molecule-MCP requires Claude Desktop to be installed and running.

Go to Claude > Settings > Developer > Edit Config > claude_desktop_config.json to include the following:

{
  "mcpServers": {
    "pymol": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/pymol_server.py"
      ]
    },
    "chimerax": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/ChimeraX_server.py"
      ]
    },
    "gromacs_copilot": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/mcp_server.py"
      ]
    }
  }
}

Install mcp and get the script

pip install "mcp[cli]" chatmol
pip install git+https://github.com/ChatMol/gromacs_copilot.git # optional, for running gromacs_copilot
which mcp

the path to mcp will be displayed. Copy this path for the next step and replace /path/to/mcp with the path to mcp.

git clone https://github.com/ChatMol/molecule-mcp.git
cd molecule-mcp
pwd

the path to molecule-mcp will be displayed. Copy this path for the next step and replace /path/to/molecule-mcp with the path to molecule-mcp.

Disclaimer

Molecule-MCP is provided "as is" without warranty of any kind, express or implied. The authors and contributors disclaim all warranties including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. Users employ this software at their own risk.

The authors bear no responsibility for any consequences arising from the use, misuse, or misinterpretation of this software or its outputs. Results obtained through Molecule-MCP should be independently validated prior to use in research, publications, or decision-making processes.

This software is intended for research and educational purposes only. Users are solely responsible for ensuring compliance with applicable laws, regulations, and ethical standards in their jurisdiction.

molecule-mcp FAQ

How do I install Molecule-MCP?

Install Claude Desktop, then configure claude_desktop_config.json to include Molecule-MCP server commands for tools like PyMOL and ChimeraX.

Does Molecule-MCP support multiple molecular tools?

Yes, it supports integration with tools such as PyMOL, ChimeraX, and Gromacs for comprehensive molecule modeling.

Can Molecule-MCP work with AI models other than Claude?

While optimized for Claude, Molecule-MCP can be adapted to work with other LLMs like OpenAI's GPT-4 and Anthropic's Claude.

What is required to run Molecule-MCP?

You need Claude Desktop running and properly configured MCP server commands pointing to the molecule-mcp scripts.

How does Molecule-MCP enhance molecule modeling?

It allows AI models to directly interact with molecular tools, enabling prompt-driven, interactive molecule design and analysis.

Is Molecule-MCP secure for scientific data?

Yes, MCP protocol principles ensure scoped, secure, and observable interactions between AI and molecular tools.

Can I extend Molecule-MCP to other molecular software?

Yes, you can add new MCP server adapters to integrate additional molecular science tools.