Molclaw Protein Protein Mmpbsa

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

This skill guides agents through the protein-protein MM/GB(PB)SA pipeline with enforced MCP handoffs, file validation, and optional analysis.

Canonical Toolchain & References

1. Step 1 — fix_pdb (reference_fix_pdb.md): repair the protein-protein complex and emit a cleaned PDB.
2. Step 2 — prepare_protein_md (reference_prepare_protein_md.md): build the protein-only MD workspace with the requested MD duration.
3. Step 3 — gmx_mmpbsa_propro (reference_gmx_mmpbsa_propro.md): compute GB/PB binding energies inside the prepared workspace.
4. Optional Step 4 — analyze_mmpbsa (reference_analyze_mmpbsa.md): aggregate the CSV/plot outputs into a final report.

MCP Tool Names (must use)

• fix_pdb
• prepare_protein_md
• gmx_mmpbsa_propro
• analyze_mmpbsa (optional)

Entry / Data Handover

Pre-flight checks

• Confirm the raw protein-protein complex PDB and associated restraints are accessible before calling fix_pdb.
• Decide whether enable_analysis will turn on Step 4 ahead of gmx_mmpbsa_propro.
• Keep dry_run=False for any production-grade binding energy request; use dry run only during validation loops.
• Prefer a validated quick profile first (md_time=20, nvt_time=1, npt_time=1) to avoid long blocking runs, then scale up only if needed.

Data Handover Contract

1. fix_pdb.output_file → prepare_protein_md.protein_pdb
2. prepare_protein_md.run_dir → gmx_mmpbsa_propro.work_dir
3. Optional analysis consumes the MM/GBSA result workspace: gmx_mmpbsa_propro.output_dir → analyze_mmpbsa.work_dir
4. gmx_mmpbsa_propro.output_files (e.g., gb_result_csv, pb_result_csv) are the canonical GB/PB summaries for downstream reporting.

Never request users to provide intermediate GROMACS artifacts (em.gro, md.xtc, md.tpr, topol.top); those files are generated inside the MCP-managed workspace.

Common MCP Client

import json
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession

class DrugSDAClient:
    def __init__(self, server_url: str):
        self.server_url = server_url
        self.session = None

    async def connect(self):
        self.transport = streamablehttp_client(url=self.server_url)
        self.read, self.write, self.get_session_id = await self.transport.__aenter__()
        self.session_ctx = ClientSession(self.read, self.write)
        self.session = await self.session_ctx.__aenter__()
        await self.session.initialize()

    async def disconnect(self):
        if self.session:
            await self.session_ctx.__aexit__(None, None, None)
        if hasattr(self, "transport"):
            await self.transport.__aexit__(None, None, None)

    @staticmethod
    def parse_result(result):
        if hasattr(result, "content") and result.content and hasattr(result.content[0], "text"):
            return json.loads(result.content[0].text)
        return result

Step-by-step Execution Details

Step 1: fix_pdb

• Entry checks
  • Verify the complex PDB and supporting files are reachable and correspond to the intended chains.
  • Disable dry_run when producing deliverable energies, toggle add_hydrogens per structural requirements.
• Success criteria
  • status == "success" and output_file contains a non-empty path.
  • atom_count, residue_count, and chain_count provide diagnostics for downstream validation.
  • On failure, return msg and abort before Step 2.

Step 2: prepare_protein_md

• Entry checks
  • Accept protein_pdb = fix_pdb.output_file as input.
  • full_md=True is enforced for this workflow, and temperature, nvt_time, and npt_time must align with resource limits.
• Success criteria
  • status == "success" and run_dir contains the expected MD workspace.
  • Ensure the required files (em.gro, md.xtc, md.tpr, topol.top) exist inside run_dir before Step 3.
  • files lists the produced artifacts for troubleshooting.

Step 3: gmx_mmpbsa_propro

• Entry checks
  • work_dir is the validated prepare_protein_md.run_dir and still contains the MD artifacts.
  • Default to method="gb" for quick runs or method="both" when PB outputs are also desired.
  • Keep skip_mmpbsa=False unless agents explicitly plan to build indexes only.
• Success criteria
  • status is "success" or "partial_success"; keep the latter when one method fails.
  • output_files.gb_result_csv and/or output_files.pb_result_csv capture the FINAL_RESULTS.* summary.
  • metrics aggregates the binding energies parsed from GB/PB outputs.

Step 4: analyze_mmpbsa (optional)

• Entry checks
  • enable_analysis must be true and work_dir must point to a gmx_mmpbsa_propro.output_dir that houses the mmgbsa/mmpbsa directories.
  • Use work_dir = gmx_mmpbsa_propro.output_dir instead of the MD preparation directory.
• Success criteria
  • status == "success" and reports lists CSV/PNG/MD artifacts produced under output_dir.
  • detected_mode clarifies whether dual, PB-only, or GB-only data were compiled.
• Fallback behavior
  • If analysis fails, keep Step 3 outputs as the workflow deliverable, log the analyzer msg, and report missing_files in the summary.
  • Retry gmx_mmpbsa_propro with the missing method before rerunning the analyzer if a branch is absent.

Agent Flow

• fix_pdb.output_file feeds prepare_protein_md.protein_pdb.
• prepare_protein_md.run_dir is the canonical gmx_mmpbsa_propro.work_dir.
• gmx_mmpbsa_propro.output_dir is the canonical analyze_mmpbsa.work_dir.
• gmx_mmpbsa_propro.output_files.gb_result_csv/pb_result_csv are the verified binding energy CSVs; both should be reported when method="both".
• Optional analyze_mmpbsa.output_dir contains the final plots/tables enumerated in reports/files, and detected_mode/missing_files explain data coverage.

Recommended Sequential Calling

client = DrugSDAClient("http://180.184.86.2:32208/mcp")
await client.connect()

# Step 1: fix_pdb
r1 = client.parse_result(await client.session.call_tool(
    "fix_pdb",
    arguments={
        "input_path": "protein_protein_complex.pdb",
        "add_hydrogens": True,
        "ph": 7.0,
        "remove_heterogens": False,
        "remove_water": False,
        "replace_nonstandard": False,
        "add_missing_residues": False,
        "dry_run": False,
    },
))
fixed_pdb = r1["output_file"]

# Step 2: prepare_protein_md
r2 = client.parse_result(await client.session.call_tool(
    "prepare_protein_md",
    arguments={
        "protein_pdb": fixed_pdb,
        "full_md": True,
        "md_time": 20.0,
        "temperature": 300.0,
        "nvt_time": 1.0,
        "npt_time": 1.0,
    },
))
md_work_dir = r2["run_dir"]

# Validate required files before MM/PBSA
required_files = ["em.gro", "md.xtc", "md.tpr", "topol.top"]
# Agents should verify these exist under md_work_dir and return an error if missing

# Step 3: gmx_mmpbsa_propro
r3 = client.parse_result(await client.session.call_tool(
    "gmx_mmpbsa_propro",
    arguments={
        "work_dir": md_work_dir,
        "method": "gb",
        "nproc": 64,
        "skip_mmpbsa": False,
        "dry_run": False,
    },
))

# Step 4: analyze_mmpbsa (optional)
if enable_analysis:
    r4 = client.parse_result(await client.session.call_tool(
        "analyze_mmpbsa",
        arguments={
            "work_dir": r3["output_dir"],
        },
    ))

await client.disconnect()

Practical Parameter Sets

1. GB-only production run (mirrors the CLI validation command)
   • fix_pdb: {"input_path": "protein_protein_complex.pdb", "add_hydrogens": True, "dry_run": False}

• prepare_protein_md: {"protein_pdb": "protein_protein_complex_fixed.pdb", "full_md": True, "md_time": 20.0, "temperature": 300.0, "nvt_time": 1.0, "npt_time": 1.0}
• gmx_mmpbsa_propro: {"work_dir": "Protein_MD_01", "method": "gb", "nproc": 64, "skip_mmpbsa": False}
• Optional analyze_mmpbsa: {"work_dir": "gmx_mmpbsa_propro_result_dir"}

2. Dual-method variant (driven by the dual-mode CLI command)
   • fix_pdb: same as above

• prepare_protein_md: {"protein_pdb": "protein_protein_complex_fixed.pdb", "full_md": True, "md_time": 50.0, "temperature": 300.0, "nvt_time": 1.0, "npt_time": 1.0}
• gmx_mmpbsa_propro: {"work_dir": "Protein_MD_02", "method": "both", "nproc": 64, "skip_mmpbsa": False}
• Optional analyze_mmpbsa: {"work_dir": "gmx_mmpbsa_propro_result_dir"}

Agent Safety Checklist

1. Enforce full_md=True and realistic MD times before invoking the MM/PBSA stage.
2. Confirm em.gro, md.xtc, md.tpr, and topol.top exist under the run_dir; abort with missing-file names if any are absent.
3. Surface partial_success explicitly when method="both" runs complete only one branch.
4. Do not propagate dry_run=True outputs to end users.
5. If the optional analyzer fails, keep gmx_mmpbsa_propro results as the canonical output and append the analyzer msg/missing_files to the summary.
6. Do not wait indefinitely for long MD stages: report progress between steps and offer a quick-profile rerun when runtime exceeds expected limits.
7. Avoid repeated filesystem polling loops; if required files are missing after one check, fail fast and surface missing filenames.

⚠ Mandatory Download of ALL MD and MMPBSA Output Files (L3 Principles 14-15)

After EACH step in the MMPBSA pipeline, download ALL output files:

Use server_file_to_base64 for each file. Verify size > 0 after download. A pipeline step is NOT considered complete until all its output files are downloaded.

For prepare_complex output directory: List ALL files in output_dir and download every one with a recognized extension (gro, xtc, tpr, top, edr, log, pdb, csv).

⚠ Residue Numbering for Per-Residue Decomposition (L3 Principle 17)

Per-residue energy decomposition uses the numbering of the input PDB. If the task references specific residues in a different scheme (e.g., UniProt), build a mapping table using molclaw-residue-mapper BEFORE interpreting which residues are energy hotspots.

⚠ Result Plausibility (L3 Principle 9)

• Protein-ligand ΔG: typically −5 to −30 kcal/mol. Positive values suggest the ligand left the pocket during MD.
• NEVER convert MM-PBSA ΔG to Kd via ΔG = RT·ln(Kd). MM-PBSA is an approximation; only relative ranking is reliable.
• If GB and PB give opposite rankings, report BOTH and note the disagreement.