# Molclaw Protein Ligand Mmpbsa

> Execution-ready protein-ligand MM/GB(PB)SA workflow with explicit MCP handoffs and optional analysis.

- **Type:** Skill
- **Install:** `agentstack add skill-internscience-molclaw-molclaw-protein-ligand-mmpbsa`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [InternScience](https://agentstack.voostack.com/s/internscience)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [InternScience](https://github.com/InternScience)
- **Source:** https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-protein-ligand-mmpbsa

## Install

```sh
agentstack add skill-internscience-molclaw-molclaw-protein-ligand-mmpbsa
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# 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](reference_fix_pdb.md)
- `prepare_complex`: [reference_prepare_complex.md](reference_prepare_complex.md)
- `run_mmpbsa`: [reference_run_mmpbsa.md](reference_run_mmpbsa.md)
- `analyze_mmpbsa`: [reference_analyze_mmpbsa.md](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.

### Step 2: `prepare_complex`
- **Pre-flight checks**: confirm `protein` equals `fix_pdb.output_file`, `ligand` path exists, and any `pose` index is valid within the ligand file.
- **Inputs**: `protein`, `ligand`, `pose`, `gpu_ids`, `full_md`, `nvt_time`, `npt_time`, `md_time`, `ph`.
- **Optional stage**: short circuits such as `full_md=False` for quick workspace generation, but then downstream steps must adjust expectations.
- **Success criteria**: `status == "success"`, `output_dir` is non-empty, `files` contains `em.gro`/`md.xtc`/`topol.top`.
- **Fallback hints**: if GPU resources are oversubscribed, rerun with `gpu_ids` trimmed or `full_md=False`; if ligand conversion fails, switch to `.mol2` or `.pdb` input.

### Step 3: `run_mmpbsa`
- **Pre-flight checks**: `work_dir` exists and matches `prepare_complex.output_dir`; verify expected `em.gro`, `md.xtc`, and `topol.top` exist before invoking.
- **Inputs**: `work_dir`, `method` (gb/pb/both), `nproc`, `interval`, `startframe`, `endframe`, `generate_input`, `dry_run`.
- **Optional stage**: `method` controls whether GB, PB, or both runs execute; `dry_run=True` tests configuration without executing heavy compute.
- **Success criteria**: `status == "success"`, `gb_dir` or `pb_dir` is created, `results` dictionary contains energy estimates, required CSVs (`FINAL_RESULTS.csv`) exist.
- **Fallback hints**: on missing CSVs, check `nproc` limits or re-run with `generate_input=True`; if `dry_run` was left `True`, rerun with the actual run.

### Step 4: `analyze_mmpbsa` (optional)
- **Pre-flight checks**: `enable_analysis` flag `True` and `work_dir` equals `run_mmpbsa.output_dir`; confirm the CSV outputs are present.
- **Inputs**: `work_dir`.
- **Optional stage**: no extra per-file overrides are required in normal workflow usage.
- **Success criteria**: `status == "success"`, `output_dir` exists, `reports` dictionary lists generated PNG/CSV/MD artifacts.
- **Fallback hints**: treat analyzer failures as soft; log the `msg` and keep the `run_mmpbsa` results as the primary output.

## Agent Flow
1. **Protein repair → complex build**: `fix_pdb.output_file` feeds `prepare_complex.protein`, guaranteeing the complex uses the cleaned receptor.
2. **Workspace build → free-energy run**: `prepare_complex.output_dir` becomes `run_mmpbsa.work_dir`, producing both `mmgbsa/FINAL_RESULTS.csv` and `mmpbsa/FINAL_RESULTS.csv` depending on `method`.
3. **Optional analysis**: when enabled, the analyzer consumes `run_mmpbsa.output_dir` (`work_dir`) to assemble summary plots, which are then surfaced through `analyze_mmpbsa.output_dir` and `reports`.
4. **Normalized insights**: every branch funnels into the same `work_dir` CSV artifacts so downstream agents can compare GB, PB, and analyzer outputs uniformly.

## Normalized Outputs (per workflow)
- `fix_pdb`: `output_file` (cleaned receptor).
- `prepare_complex`: `output_dir`/`files` (workspace containing GROMACS artifacts).
- `run_mmpbsa`: `work_dir`, `gb_dir`, `pb_dir`, `results`, `command`.
- `analyze_mmpbsa`: `output_dir`, `reports`, `detected_mode`, `missing_files` (optional insights).

## Safety Checklist
- Never pass manual MD files instead of `prepare_complex.output_dir`.
- Treat any missing `output_file`/`output_dir` as a hard failure and stop before the next tool.
- Validate GPU/CPU resources before running long `run_mmpbsa` jobs (`nproc`, `gpu_ids`).
- If `method="both"`, ensure both PB and GB CSVs are created; otherwise, rerun with `method="pb"` or `"gb"` only.
- Surface actionable diagnostics (`missing file`, `invalid pose`, `transport error`) in the `msg` field.

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [InternScience](https://github.com/InternScience)
- **Source:** [InternScience/MolClaw](https://github.com/InternScience/MolClaw)
- **License:** MIT

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-internscience-molclaw-molclaw-protein-ligand-mmpbsa
- Seller: https://agentstack.voostack.com/s/internscience
- Browse the marketplace: https://agentstack.voostack.com/browse

---
Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.