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 — an OPLS-AA/CM1A force-field parameter generator for organic ligands, built on LigParGen.
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 for how and why.
Using this Space as an MCP tool
Besides the web form, this Space runs as an MCP 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):
{
"mcpServers": {
"ligpargen": {
"url": "https://lsdodda-ligpargen.hf.space/gradio_api/mcp/sse"
}
}
}
For a stdio-only client, bridge via mcp-remote:
{
"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.