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Molecule MCP Server

Molecule-MCP provides MCP-based control of molecular tools via Claude, enabling direct interaction and collaboration.

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Installation

Add the following to your MCP client configuration file.

Configuration

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

Molecule-MCP provides MCP-based support to connect molecular tools with Claude AI, enabling direct interaction and control of those tools as part of collaborative molecule modeling workflows.

How to use

To use Molecule-MCP, run the MCP servers locally and configure Claude Desktop to access them via MCP. Each server exposes a local runner that Molecule-MCP can invoke to integrate tools like PyMOL, ChimeraX, and GROMACS Copilot into your prompt-driven workflows.

A representative MCP configuration snippet shows how the local servers are wired to a shared MCP runner. This JSON snippet is intended to be placed in Claude Desktop's MCP configuration to register the three local services.

How to install

Prerequisites: you need Claude Desktop installed and running to use Molecule-MCP.

1. 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"
      ]
    }
  }
}

2. Install the MCP CLI 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 printed by the previous command is the MCP executable. Copy this path for the next step and replace /path/to/mcp with that value.

3. Clone the Molecule-MCP repository and locate its path:

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

The path printed here is the Molecule-MCP directory path. Copy this path for the next step and replace /path/to/molecule-mcp accordingly.

Additional notes

Disclaimer: Molecule-MCP is provided as is without warranty of any kind. The authors and contributors do not guarantee fitness for a particular purpose, and users are responsible for ensuring compliance with applicable laws and ethical standards in their jurisdiction.