Warning

Currently this work is in progress, please give us feedback here: https://github.com/omsf/skills/discussions

OMSF workflow skills

Portable Agent Skills for every workflow in the OMSF workflow directory: 16 skills covering Open Force Field, Open Free Energy, and OpenADMET.

Each <name>/SKILL.md teaches an agent when to use the workflow, what to ask for, how to prepare the environment, which steps to follow, and how to check the result. These are agent instructions, not vendored software or automated simulation pipelines. The layout follows the catalog-and-skill-directory pattern used by NVIDIA's skills repository; this project is not an NVIDIA product or an upstream certification program.

Use a skill

1. Pick a workflow below and review its instructions, especially environment and scientific limitations.

2. Copy that entire skill directory into your agent's supported skill location. For clients using project-local .agents/skills/, run from your target project:

   mkdir -p .agents/skills
   # Replace /path/to/omsf-skills with this checkout. Use a fresh destination.
   cp -R /path/to/omsf-skills/openfe-rbfe-cli .agents/skills/

   Claude Code uses .claude/skills/; other clients may use different locations. Reload or restart the client as needed. Installing a skill does not install its scientific dependencies.

3. Ask for the workflow and supply your inputs. For example:

   Use openfe-rbfe-cli to plan relative binding free energies for my aligned ligand SDF and prepared protein. Inspect the network first; do not launch simulations until I approve the settings and compute budget.

Skills are independently installable. No global tool permissions or agent-specific plugins are required by this repository.

Workflow catalog

Workflow titles match the OMSF workflow directory as retrieved 2026-10-26. Each skill links to the upstream material it was researched against. Revision pins identify source material, not a guarantee that all dependency versions remain available or compatible.

Directory workflow	Skill
Export an OpenFF OpenMM System to AMBER and GROMACS files	openff-export-amber-gromacs
Generating Partial Charges with the OpenFE CLI	openfe-partial-charges
Integrating a Sage ligand with an Amber protein	openff-sage-amber-protein
OpenADMET Data Catalogs	openadmet-data-catalogs
OpenADMET Showcase	openadmet-showcase
OpenFE Showcase	openfe-showcase
OpenFF Example: Conformer Energies	openff-conformer-energies
OpenFF Example: Forcefield Modification	openff-forcefield-modification
OpenFF Example: Inspecting SMIRNOFF Parameters	openff-inspect-parameters
OpenFF Example: QCArchive Interface	openff-qcarchive
OpenFF Example: SMIRNOFF Simulation	openff-smirnoff-simulation
OpenFF Example: Virtual Sites Showcase	openff-virtual-sites
OpenFF Toolkit Showcase	openff-toolkit-showcase
Post Translational Modification Prototype	openff-ptm-prototype
Relative Free Energies with the OpenFE CLI	openfe-rbfe-cli
Visualizations with OpenFF	openff-visualization

Warnings

This is an ALPHA implementation of this repository and is provided as is. A successful example run is not evidence of convergence, predictive accuracy, or suitability for clinical or regulatory decisions. Full end-to-end scientific validation is not claimed. We always recommend using project documentation for the most up-to-date workflow implementations.

Attribution and licensing

Sources and upstream license identifiers are recorded in individual skills. Those identifiers describe upstream projects, not a grant of rights to this collection or every underlying dataset. Check dataset-specific terms separately. No repository-wide license has been selected for this new collection; select one before public distribution. Upstream notebooks and datasets are linked rather than bundled.