molclaw-mmpbsa-toolkit

Files (9)

• SKILL.md
• protein-ligand-analyze-mmpbsa.md · references/
• protein-ligand-fix-pdb.md · references/
• protein-ligand-prepare-complex.md · references/
• protein-ligand-run-mmpbsa.md · references/
• protein-protein-analyze-mmpbsa.md · references/
• protein-protein-fix-pdb.md · references/
• protein-protein-gmx-mmpbsa.md · references/
• protein-protein-prepare-md.md · references/

SKILL.md (first lines)

# MM/GB(PB)SA Toolkit

## Invocation

Use the exact tool name and parameter schema exposed by the current harness. All input paths must be server-visible paths returned by earlier MolClaw tools.

## Protein-ligand path

1. `prepare_complex` consumes `protein` and `ligand` and returns an MD workspace in `output_dir`.
2. `run_mmpbsa` consumes that directory as `work_dir`; choose `method` from `gb`, `pb`, or `both`.
3. `analyze_mmpbsa` consumes the calculation output as `work_dir` and generates reports.

## Protein-protein path

1. `prepare_protein_md` consumes a protein-only complex through `protein_pdb` and returns `run_dir`.
2. `gmx_mmpbsa_propro` consumes that directory as `work_dir`; choose `method` from `gb`, `pb`, or `both`.
3. `analyze_mmpbsa` consumes the calculation output as `work_dir`.

Check each call's `status`, preserve returned directories exactly, and do not treat dry-run outputs as scientific results. Detailed protein-ligand and protein-protein handoff and recovery notes are retained under this skill's `references/` directory; read only the relevant files when needed.

From InternScience/MolClaw, MIT.

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