schrodinger-mcp

An MCP server that exposes Schrödinger Suites 2026 computational-chemistry / drug-discovery workflows to Claude (Claude Code and Claude Desktop). Ask Claude to fetch a PDB, prep a protein and ligands, build a Glide grid, dock, score, run ADMET, MM-GBSA, or QM — 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.

Claude ──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.

Related MCP server: PyMOL-MCP-Vis

Requirements

• macOS/Linux with Schrödinger Suites 2026 installed and licensed (auto-detected at /opt/schrodinger/suites*, or set SCHRODINGER).

• uv (recommended) or pip.

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

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

Sanity check:

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

Register with Claude

Claude Code (the -- separates the launch command; quote the spaced path):

claude mcp add schrodinger \
  --env SCHRODINGER=/opt/schrodinger/suites2026-1 \
  -- "/Users/mac/schrodinger mcp/.venv/bin/schrodinger-mcp"

Claude Desktop — add to ~/Library/Application Support/Claude/claude_desktop_config.json:

{
  "mcpServers": {
    "schrodinger": {
      "command": "/Users/mac/schrodinger mcp/.venv/bin/schrodinger-mcp",
      "args": [],
      "env": { "SCHRODINGER": "/opt/schrodinger/suites2026-1" }
    }
  }
}

Restart the client; the schrodinger tools and the schrodinger://installation resource appear.

Tools

Foundation (synchronous)

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

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

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.