schrodinger-maestro-driver

Schrodinger / Maestro Driver

Overview

The schrodinger MCP server is a thin, security-conscious wrapper over a local Schrodinger Suite install. It NEVER imports the schrodinger package in-process; every tool builds an argv list and hands it to a single internal _exec() chokepoint that runs WITHOUT a shell. Client-supplied paths are validated by _safe_path() (rejects empty/flag-like values, normalizes to absolute) before reaching any argv, so there is no shell or argument injection. The run_schrodinger_python tool is an intentional arbitrary-code escape hatch - this server is for local, single-user use only.

• Source: C:\Users\agentuser\source\repos\schrodinger-mcp\server.py (+ _sch_helper.py, which runs INSIDE the Schrodinger interpreter where both schrodinger and a bundled rdkit are importable).
• Verified install: Schrodinger 2022-4, build 79134, at D:\Program Files\Schrodinger 2022-4.

Environment Setup

The server reads SCHRODINGER from the environment; it defaults to the Windows path D:\Program Files\Schrodinger 2022-4 and on POSIX you must set it.

• MCP registration (verified, stdio):
  • command: C:\Users\agentuser\source\repos\schrodinger-mcp\.venv\Scripts\python.exe
  • args: C:\Users\agentuser\source\repos\schrodinger-mcp\server.py
  • env: SCHRODINGER = D:\Program Files\Schrodinger 2022-4
• Cross-platform note: the server resolves run.exe/driver .exe on Windows and falls back to the extension-less run/driver names on POSIX. On POSIX, export SCHRODINGER to your suite root (e.g. /opt/schrodinger/suites/2022-4).

The 12 Tools (grouped by license cost)

Typical Workflow (end-to-end structure-based screening)

Full pipeline is now in-server (receptor prep -> grid -> dock -> rescore)

Common Mistakes

Related Skills