agentmods.dev

nonstd-residue

nonstd-residue is a skill for Claude Code, Codex from CharlesHahn/DuIvySkills. It costs 240 tokens per session (4,684 once invoked), scanned A, original, GPL-3.0.

A workflow guide for creating GROMACS force-field definitions for non-standard amino-acid residues, such as a chemically modified cysteine. A force field is the set of rules and parameters used to calculate molecular interactions in a simulation.

In plain words
What is it for?
Use it to turn Sobtop-generated ITP files into residue and hydrogen-bond definitions, register GAFF parameters in a local force-field copy, assemble a PDB structure, and run pdb2gmx.
Why use it?
It provides the required steps when standard residue definitions cannot represent a covalent modification. This helps connect existing charge and topology data to a usable GROMACS residue and force field.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

not rated 22repo 2mo ago A scan 240 tokens GPL-3.0

Good fit Use it to turn Sobtop-generated ITP files into residue and hydrogen-bond definitions, register GAFF parameters in a local force-field copy, assemble a PDB structure, and run pdb2gmx.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/charleshahn/duivyskills/nonstd-residue
View source ↗ CharlesHahn/DuIvySkills
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add CharlesHahn/DuIvySkills --skill nonstd-residue
Clone the repo
git clone --depth 1 https://github.com/CharlesHahn/DuIvySkills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for nonstd-residue

README.md
[![agentmods](https://agentmods.dev/badge/skills/charleshahn/duivyskills/nonstd-residue/github.svg)](https://agentmods.dev/skills/charleshahn/duivyskills/nonstd-residue)
Your own site
<a href="https://agentmods.dev/skills/charleshahn/duivyskills/nonstd-residue"><img src="https://agentmods.dev/badge/skills/charleshahn/duivyskills/nonstd-residue/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for nonstd-residue

Your own site · 80×15
<a href="https://agentmods.dev/skills/charleshahn/duivyskills/nonstd-residue"><img src="https://agentmods.dev/badge/skills/charleshahn/duivyskills/nonstd-residue.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 240 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,684 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00240 $0.04684
Opus 5.5 $0.00096 $0.01874
Sonnet 5.5 $0.00048 $0.00937
Haiku 4.5 $0.00024 $0.00468

Measured 2mo ago against content hash 295cc1f62721, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

nonstd-residue scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

The scan reads SKILL.md. This mod also ships 14 executable files (examples/cyb/adversarial_review.py, examples/cyb/compare_ff.py, examples/cyb/run_all.sh, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

nonstd-residue/SKILL.md · 367 lines

The source is not reproduced here

Licensed GPL-3.0

The repository is licensed GPL-3.0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.

Read it on GitHub

Files

What ships with it

60 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2mo ago First seen · 367 lines · 240 tokens per session scan A 295cc1f62721

Subscribe to this mod's changes

nonstd-residue is a skill published in the GitHub repository CharlesHahn/DuIvySkills (22 stars, last pushed 2mo ago), licensed GPL-3.0. It adds 240 tokens to every session and 4,684 once invoked, about $0.0010 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientific
Related

nonstd-residue compared with skills from other repositories

nonstd-residue next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
nonstd-residueCharlesHahn/DuIvySkillsSkill222mo agoGPL-3.0A240Claude Code, Codex
instrument-data-to-allotropeanthropics/knowledge-work-pluginsSkill35k2d agoApache-2.0A123Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA83Claude Code
matlabK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA44Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA71Claude Code, Codex
research-engineerdavila7/claude-code-templatesSkill33kyesterdayMITA43Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmedSkill5.8kyesterdayApache-2.0A205Claude Code