molclaw-protein-ligand-mmpbsa

Protein-Ligand MM/PBSA Workflow (Execution-Ready)

Note:

• Local files are not directly accessible by the server. Please upload them to the server using molclaw-file-transfer before execution.
• For PDB file inputs, it is recommended to preprocess them using molclaw-pdbfixer before execution.
• Please refer to skill molclaw-scp-server to complete tool invocation.

Canonical Toolchain

1. fix_pdb → cleans the receptor and returns output_file.
2. prepare_complex → consumes the repaired protein plus ligand to build the MD workspace and writes output_dir.
3. run_mmpbsa → consumes work_dir to execute GB/PB calculations and emits CSV summaries.
4. analyze_mmpbsa (optional) → consumes run_mmpbsa.output_dir to derive plots/reports from the MM/PBSA results.

SCP Tool Names (must use)

• fix_pdb
• prepare_complex
• run_mmpbsa
• analyze_mmpbsa

Tool References

• fix_pdb: reference_fix_pdb.md
• prepare_complex: reference_prepare_complex.md
• run_mmpbsa: reference_run_mmpbsa.md
• analyze_mmpbsa: reference_analyze_mmpbsa.md

Data Handover Contract

1. fix_pdb.output_file → prepare_complex.protein (never substitute with manual paths).
2. prepare_complex.output_dir → run_mmpbsa.work_dir (required to contain em.gro, md.xtc, md.tpr, topol.top, ligand files).
3. run_mmpbsa.output_dir → analyze_mmpbsa.work_dir when analysis is enabled.

Step Details

Step 1: fix_pdb

• Pre-flight checks: ensure input_path exists and is a readable PDB; dry_run defaults to False so the file is written unless explicitly skipping.
• Inputs: input_path, add_hydrogens, remove_water, replace_nonstandard, add_missing_residues, dry_run.
• Optional stage: set keep_chains to restrict the repair when a subset of chains is needed.
• Success criteria: status == "success", output_file is populated, atom/residue counts report >0.
• Fallback hints: replay the msg, mention which residue/chain failed, or rerun with dry_run=True to diagnose before writing.