schrodinger-mcp

<p align="center"> <img src="docs/hero.png" alt="schrodinger-mcp — drive Schrödinger drug-discovery workflows from your AI agent" width="540"> </p>

An MCP server that exposes Schrödinger Suites computational-chemistry / drug-discovery workflows to any MCP-capable coding agent — Claude Code, Claude Desktop, Cursor, GitHub Copilot, OpenCode, Cline, Windsurf, Zed, and more. Ask your agent to fetch a PDB, prep a protein and ligands, build a Glide grid, dock, score, run ADMET, MM-GBSA, QM, or draw a 2D interaction diagram — it drives Schrödinger for you and hands back ranked tables plus files you can open in Maestro.

How it works

The server runs in its own virtualenv (any Python ≥3.10) and shells out to $SCHRODINGER/run for all chemistry. Its MCP dependencies therefore stay independent of Schrödinger's bundled Python 3.11. Fast operations return inline; long jobs run under a detached supervisor that survives server restarts, and you poll them with get_job_status / get_job_results.

MCP client ──tool call──▶ schrodinger-mcp (venv, FastMCP, stdio)
                            │  fast ops ─▶ $SCHRODINGER/run python3 <worker>  ─▶ JSON
                            └  long jobs ─▶ detached supervisor ─▶ $SCHRODINGER/<launcher> -WAIT
                                             └─ status.json (authoritative) ◀─ poll

Outputs are written under ~/.local/share/schrodinger-mcp/ (override with SCHRODINGER_MCP_HOME) and every tool also returns a structured summary.

Requirements

• macOS, Linux, or Windows with Schrödinger Suites installed and licensed. Any recent release works — the server auto-detects the newest installed version (globbing /opt/schrodinger/suites* or C:\Program Files\Schrodinger*) and reports it via detect_installation. Set SCHRODINGER to pin a specific release.
• uv (recommended) or pip.

Version support: developed and validated against Suites 2026-1, but the server is version-agnostic — it discovers whatever release is installed and calls stable CLI/Python interfaces (with fallbacks for API calls that moved between releases). Tool flags target modern releases; on much older versions a flag may occasionally need a tweak.

This project contains no Schrödinger software or data. You must supply your own licensed installation of Schrödinger Suites; this server only invokes it through its documented $SCHRODINGER/run / CLI interfaces.

GPU note: Desmond molecular dynamics and FEP+ require an NVIDIA/CUDA GPU and are intentionally not exposed — they are not practical on Apple Silicon / non-NVIDIA hosts.

Install

macOS / Linux

cd schrodinger-mcp
uv venv --python 3.12 .venv
source .venv/bin/activate
uv pip install -e ".[dev]"

Windows (PowerShell)

cd schrodinger-mcp
uv venv --python 3.12 .venv
.venv\Scripts\activate
uv pip install -e ".[dev]"

The install root is auto-detected per platform (/opt/schrodinger/suites* on macOS/Linux, C:\Program Files\Schrodinger* on Windows). Set SCHRODINGER to override.

Sanity check:

python -c "from schrodinger_mcp.tools.foundation import detect_installation as d; print(d()['version'])"

Connect a coding agent

This is a standard stdio MCP server, so any MCP-capable client works. In every case you point the client at the console script and set the SCHRODINGER env var. Use the absolute path to the installed command:

Platform	Server command (<CMD> below)
macOS / Linux	/Users/mac/schrodinger mcp/.venv/bin/schrodinger-mcp
Windows	C:\path\to\schrodinger-mcp\.venv\Scripts\schrodinger-mcp.exe

And <ROOT> = your install root (/opt/schrodinger/suites2026-1, or C:\Program Files\Schrodinger2026-1). After configuring, restart the client; the schrodinger tools and the schrodinger://installation resource appear.

Claude Code

claude mcp add schrodinger --env SCHRODINGER=<ROOT> -- "<CMD>"

Cursor · Claude Desktop · Cline · Windsurf (shared mcpServers format)

These four use the same JSON shape — just a different file:

Client	Config file
Cursor	~/.cursor/mcp.json (global) or .cursor/mcp.json (per project)
Claude Desktop	~/Library/Application Support/Claude/claude_desktop_config.json (macOS) · %APPDATA%\Claude\claude_desktop_config.json (Windows)
Cline (VS Code)	the “Configure MCP Servers” panel → cline_mcp_settings.json
Windsurf	~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "schrodinger": {
      "command": "<CMD>",
      "args": [],
      "env": { "SCHRODINGER": "<ROOT>" }
    }
  }
}

GitHub Copilot (VS Code agent mode)

Create .vscode/mcp.json in the workspace (or run “MCP: Add Server” from the Command Palette), then enable it in the Copilot Chat Agent mode tool picker:

{
  "servers": {
    "schrodinger": {
      "type": "stdio",
      "command": "<CMD>",
      "args": [],
      "env": { "SCHRODINGER": "<ROOT>" }
    }
  }
}

OpenCode

Add to opencode.json (project root) or ~/.config/opencode/opencode.json:

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "schrodinger": {
      "type": "local",
      "command": ["<CMD>"],
      "environment": { "SCHRODINGER": "<ROOT>" },
      "enabled": true
    }
  }
}

Zed

In settings.json (context_servers):

{
  "context_servers": {
    "schrodinger": {
      "command": { "path": "<CMD>", "args": [], "env": { "SCHRODINGER": "<ROOT>" } },
      "settings": {}
    }
  }
}

Any other MCP client

Transport stdio, command <CMD>, one environment variable SCHRODINGER=<ROOT>. That's all the server needs. (On Windows use doubled backslashes inside JSON strings.)

Inline images: the 2D-structure and interaction-diagram tools return MCP image content. Claude clients render it inline; other agents may show it as an attachment or just return the result — either way the PNG is always written to disk and its path is returned, so nothing is lost.

Tools

Foundation (synchronous)

Tool	What it does
detect_installation	Report root, version, installed workflows, hosts, GPU
fetch_pdb	Download a structure from RCSB by 4-char PDB ID
convert_structure	Convert between mae/maegz/sdf/pdb/mol2/smi/cif
structure_info	Counts, titles, charges, MW, chains, properties
smiles_to_3d	Quick single-conformer 3D from SMILES
split_structures / merge_structures	Split a multi-structure file / concatenate

Preparation (async) — ligprep, protein_prepwizard, epik, confgen

Glide docking — generate_glide_grid, glide_dock (SP/XP), summarize_docking (sync)

ADMET & site analysis — qikprop, compute_descriptors (sync), sitemap, shape_screen

QM & MM-GBSA — prime_mmgbsa, jaguar_qm

Visualization (sync) — render_2d_structure (2D depiction PNG), analyze_interactions (H-bonds / salt bridges / π-π / π-cation report), ligand_interaction_diagram (2D interaction map PNG with residues labelled), render_3d_view (self-contained interactive 3D viewer HTML — rotate/zoom/share a protein-ligand pose with H-bonds drawn, no Maestro needed), generate_2d_report (PDF/HTML of structures with properties)

Async job control — get_job_status, get_job_results, cancel_job, list_jobs

Async tools return a job_id immediately. Poll get_job_status(job_id) until state == "completed", then get_job_results(job_id) for the output files.

Example: dock a ligand against a target

1. fetch_pdb("1HSG")                     → receptor.pdb
2. protein_prepwizard(receptor.pdb)      → job → prepared.maegz
3. ligprep("CC(=O)Oc1ccccc1C(=O)O")      → job → ligprep_out.maegz
4. generate_glide_grid(prepared, center=[x,y,z] or ligand_ref=...) → job → grid.zip
5. glide_dock(grid.zip, ligprep_out, precision="SP")  → job → dock_pv.maegz
6. summarize_docking(dock_pv.maegz)      → ranked GlideScore table

Testing

pytest tests/test_unit.py -q            # fast unit tests, no Schrödinger needed
python tests/manual_docking_e2e.py      # real end-to-end docking (bundled fixture, ~3 min)
python tests/manual_wave5.py            # qikprop / MM-GBSA / sitemap / shape / jaguar

Inspect the live MCP server with the official inspector:

npx @modelcontextprotocol/inspector "/Users/mac/schrodinger mcp/.venv/bin/schrodinger-mcp"

Configuration

Env var	Default	Purpose
SCHRODINGER	autodetect	Install root
SCHRODINGER_MCP_HOME	~/.local/share/schrodinger-mcp	Job dirs, scratch, registry
SCHRODINGER_MCP_MAX_JOBS	2	Concurrent heavy-job advisory limit
SCHRODINGER_MCP_SYNC_TIMEOUT	120	Seconds before a sync op suggests going async

Disclaimer & trademarks

This is an independent, unofficial project. It includes no Schrödinger software, source, or data, and requires a separately licensed Schrödinger Suites installation.

Schrödinger, Maestro, Glide, Desmond, Jaguar, Prime, QikProp, Epik, Phase, Canvas, and SiteMap are trademarks of Schrödinger, LLC. This project is not affiliated with, endorsed by, or sponsored by Schrödinger, LLC; product names are used only to describe interoperability. Use of Schrödinger software is governed by your own license agreement with Schrödinger — consult it before publishing benchmarks or results.

License

MIT © 2026. Your use of the underlying Schrödinger Suites remains subject to your Schrödinger license.