The Agent Skills Directory

[INDIRECT_PROMPT_INJECTION]: The skill ingests external datasets (PDB files, SMILES strings, and trajectory files) which serve as entry points for untrusted data. \n- Ingestion points: pdb_file and smiles parameters in SKILL.md; topology_file and trajectory_file in references/mdanalysis_analysis.md. \n- Boundary markers: The Agent Operating Procedure (AOP) explicitly mandates environment checks, input pinning, and molecule sanitization. \n- Capability inventory: The skill utilizes file system access to write simulation logs, binary trajectories (DCD), and structural files (PDB). \n- Sanitization: Integration with PDBFixer ensures that raw PDB files are cleaned, standardized, and repaired before simulation. \n- [EXTERNAL_DOWNLOADS]: The skill references several well-known scientific documentation sites and repositories (e.g., openmm.org, mdanalysis.org, charmm-gui.org) to provide the agent with authoritative reference material. These are standard resources within the computational chemistry community. \n- [COMMAND_EXECUTION]: The skill includes instructions for package installation using established package managers (conda, uv pip). The commands target standard, reputable scientific packages.

molecular-dynamics