MCP Setup

AutoSolvate can run an MCP server for agent integrations (GitHub Copilot, Claude, etc.). This section explains how to generate a ready-to-use MCP config and add it to your editor.

Prerequisites (optional)

FastMCP is optional. Install it only if you want to run the MCP server:

conda install -c conda-forge fastmcp

Or with pip:

pip install fastmcp

Generate MCP JSON

From the environment where AutoSolvate is installed:

autosolvate mcp_json --full > mcp.json

For a long-running HTTP MCP server (recommended for frameworks that do not want the server lifecycle tied to a stdio pipe), generate an HTTP config instead:

autosolvate mcp_json --full --transport streamable-http --host 127.0.0.1 --port 8000 > mcp.json

This command:

Detects the active Python executable and environment prefix.
Populates AMBERHOME, PATH, and LD_LIBRARY_PATH when available.
Emits warnings to stderr if key executables are missing.
For HTTP configs, prints the recommended autosolvate mcp_server … startup command to stderr.

Use the config in VS Code

Paste the generated server block into your VS Code (or other agent) MCP config (usually .vscode/mcp.json). Example:

{
  "servers": {
    "autosolvate-local": {
      "type": "stdio",
      "command": "/path/to/python",
      "args": ["-m", "autosolvate", "mcp_server", "--transport", "stdio"],
      "env": {
        "PYTHONUNBUFFERED": "1",
        "AMBERHOME": "/path/to/env",
        "PATH": "/path/to/env/bin:${env:PATH}",
        "LD_LIBRARY_PATH": "/path/to/env/lib:${env:LD_LIBRARY_PATH}"
      }
    }
  },
  "inputs": []
}

HTTP configuration example:

{
  "servers": {
    "autosolvate-local": {
      "type": "http",
      "url": "http://127.0.0.1:8000/mcp"
    }
  },
  "inputs": []
}

Run the HTTP server separately

If you choose HTTP transport, start the server in a terminal before connecting your MCP client:

autosolvate mcp_server --transport streamable-http --host 127.0.0.1 --port 8000

streamable-http is usually the best choice for persistent integrations such as LangChain adapters, because the AutoSolvate process is no longer tied to a stdio pipe owned by the caller.

Notes

If AMBERHOME is not detected, set it manually to your AmberTools prefix.
Ensure packmol, antechamber, and tleap are available in the same environment.

You can rename the server via:

autosolvate mcp_json --full --server-name autosolvate-local

You can customize the HTTP endpoint path if needed:

autosolvate mcp_json --full --transport streamable-http --host 127.0.0.1 --port 8000 --path /mcp