| --- |
| title: LigParGen |
| emoji: 🧪 |
| colorFrom: blue |
| colorTo: green |
| sdk: docker |
| app_port: 7860 |
| pinned: false |
| tags: |
| - mcp-server |
| --- |
| |
| # LigParGen |
|
|
| A Hugging Face Space mirroring the core of [zarbi.chem.yale.edu/ligpargen](https://zarbi.chem.yale.edu/ligpargen/) — an OPLS-AA/CM1A force-field parameter generator for organic ligands, built on [LigParGen](https://github.com/leelasd/LigParGen_2.3). |
|
|
| Submit a molecule by SMILES, by drawing a structure, or by uploading a PDB/MOL file, and get back parameter/topology files for OpenMM, GROMACS, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, and BOSS/MCPRO — plus a 3D preview of the optimized geometry. |
|
|
| BOSS is proprietary software supplied to this Space at runtime from a private, access-controlled store — see `docs/adr/0001` and `docs/adr/0003` in the [main repo](https://github.com/leelasd/LigParGen_2.3) for how and why. |
|
|
| ## Using this Space as an MCP tool |
|
|
| Besides the web form, this Space runs as an [MCP](https://modelcontextprotocol.io) server (Gradio's built-in `mcp_server=True`), so an MCP-aware agent can call `run_ligpargen` directly instead of a human filling out the form. Same 200-atom limit, job timeout, and rate limit as the UI apply. |
|
|
| SSE endpoint: |
|
|
| ``` |
| https://lsdodda-ligpargen.hf.space/gradio_api/mcp/sse |
| ``` |
|
|
| For an SSE-capable client (e.g. Claude Desktop's `mcpServers` config): |
|
|
| ```json |
| { |
| "mcpServers": { |
| "ligpargen": { |
| "url": "https://lsdodda-ligpargen.hf.space/gradio_api/mcp/sse" |
| } |
| } |
| } |
| ``` |
|
|
| For a stdio-only client, bridge via [`mcp-remote`](https://www.npmjs.com/package/mcp-remote): |
|
|
| ```json |
| { |
| "mcpServers": { |
| "ligpargen": { |
| "command": "npx", |
| "args": ["mcp-remote", "https://lsdodda-ligpargen.hf.space/gradio_api/mcp/sse"] |
| } |
| } |
| } |
| ``` |
|
|
| The running Space also has its own "MCP" tab (bottom of the page) with the same endpoint and a live tool schema. |
|
|
