protein-tools-mcp

Overview Schema Source Related Servers Discussions Admin

check_metal_params

Scan GROMACS force-field directories or .itp/.ff files for metal atomtypes, reporting sigma/epsilon or MISSING entries before pdb2gmx to prevent metalloprotein topology build failures.

Instructions

Scan a GROMACS force-field directory or .itp/.ff file for metal atomtypes (e.g. ZN, FE) and report sigma/epsilon or MISSING entries.

Run this BEFORE pdb2gmx on any metalloprotein - a missing metal atomtype will kill the topology build.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "ff_path": "<ff_path>"
    },
    "name": "check_metal_params"
  }
}

Input Schema

Name	Required	Description	Default
`metals`	No		ZN,FE
`ff_path`	Yes

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

A4.2/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the behavioral burden and does well: it discloses what is reported (sigma/epsilon values or MISSING entries), the failure mode it guards against, and its workflow position. It leaves read-only/local-scan nature implicit rather than stated, so not a 5.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two tight sentences with no filler, and the scan-and-report behavior is front-loaded ahead of the prerequisite guidance.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values need no explanation, and the pre-flight purpose is fully covered. The only gap is the undocumented metals parameter, which leaves a small hole for a 2-parameter tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0%, so the description must compensate. It explains ff_path well (a force-field directory or .itp/.ff file), but the metals parameter and its 'ZN,FE' default are never mentioned in the description—the 'e.g. ZN, FE' example hints at it without documenting the parameter or its comma-separated syntax.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb (scan) plus the exact resource (GROMACS force-field directory or .itp/.ff file) and the output content (sigma/epsilon or MISSING entries). It is easily separable from sibling tools like metal_geometry and query_metal_sites, which deal with sites/geometry rather than force-field atomtypes.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicitly says to run this BEFORE pdb2gmx on any metalloprotein, and gives the consequence of skipping it (a missing metal atomtype kills the topology build). It does not name alternative sibling tools or state when-not to use it, so it falls short of a full 5.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.