bio-mcp-amber

bio-mcp/bio-mcp-amber

3.2

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This document provides a structured summary of the MCP server for the AMBER molecular dynamics suite, which facilitates PDB relaxation and molecular dynamics simulations.

Tools

  1. amber_relax_pdb

    Perform energy minimization and relaxation of PDB structures using AMBER.

bio-mcp-amber

MCP (Model Context Protocol) server for AMBER molecular dynamics suite for PDB relaxation.

Overview

This MCP server provides access to AMBER functionality, allowing AI assistants to perform molecular dynamics simulations and PDB structure relaxation.

Features

  • PDB structure relaxation and energy minimization
  • Molecular dynamics simulations for protein structures
  • File size limits and timeout protection
  • Temporary file management
  • Async execution with proper error handling

Installation

Using pip

pip install bio-mcp-amber

From source

git clone https://github.com/bio-mcp/bio-mcp-amber
cd bio-mcp-amber
pip install -e .

Configuration

Configure your MCP client (e.g., Claude Desktop) by adding to your configuration:

{
  "mcp-servers": {
    "bio-amber": {
      "command": "python",
      "args": ["-m", "bio_mcp_amber"]
    }
  }
}

Environment Variables

  • BIO_MCP_MAX_FILE_SIZE: Maximum input file size (default: 100MB)
  • BIO_MCP_TIMEOUT: Command timeout in seconds (default: 300)
  • BIO_MCP_AMBER_PATH: Path to amber executable
  • BIO_MCP_PMEMD_PATH: Path to pmemd executable (GPU-accelerated version)

Usage

Once configured, the AI assistant can use the following tools:

amber_relax_pdb

Perform energy minimization and relaxation of PDB structures using AMBER.

Parameters:

  • input_file (required): Path to input PDB file
  • force_field (optional): Force field to use (default: ff19SB)
  • steps (optional): Number of minimization steps (default: 10000)
  • restraints (optional): Apply positional restraints to backbone atoms

Example:

Relax structure.pdb using AMBER with ff19SB force field and 10000 minimization steps

Development

Running tests

pytest tests/

Building Docker image

docker build -t bio-mcp-amber .

License

MIT License