Agent skill

Packmol

Generate initial configurations for molecular simulations using Packmol.

AGPL-3.0Auto-check passedResearch & Science

Install Packmol

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill packmol -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG packmol --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/packmol .claude/skills/packmol && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "packmol" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/packmol into .claude/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/packmol

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill packmol -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG packmol --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.claude/skills/packmol .agents/skills/packmol && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "packmol" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/packmol into .agents/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill packmol -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG packmol --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.claude/skills/packmol .cursor/skills/packmol && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "packmol" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/packmol into .cursor/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/Hello-QM/catgo-LRG.git --path .claude/skills/packmol

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill packmol -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG packmol --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.claude/skills/packmol .gemini/skills/packmol && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "packmol" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/packmol into .gemini/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG packmol

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill packmol -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .github/skills && cp -r skills-src/.claude/skills/packmol .github/skills/packmol && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "packmol" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/packmol into .github/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill packmol -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG packmol --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.claude/skills/packmol .opencode/skills/packmol && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "packmol" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/packmol into .opencode/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: packmol
GitHub stars: 205
Token cost: ~1.1k tokens
SKILL.md length: 346 words
Files: 1
Skills in repo: 75
Repo updated: Sep 22, 2026
First seen: Oct 7, 2026
Licence: AGPL-3.0

At a glance

Generate initial configurations for molecular simulations using Packmol.

Works in 2 steps: Prepare molecule files → Create Packmol input and run
Tasks that involve Drug discovery and cheminformatics
SKILL.md covers When to Use, Prerequisites, Workflow Steps and Packmol Input Template —…, plus 6 more sections
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Packmol is an agent skill from Hello-QM/catgo-LRG. Generate initial configurations for molecular simulations using Packmol. Build liquid boxes, mixtures, solutions, and solvated systems by packing molecules into a defined region.

Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts. Compatibility notes: Requires Packmol installed (apt install packmol or compiled from source). Input molecules must be in PDB or XYZ format.

It sits in Research & Science, covering Drug discovery and cheminformatics. The repository describes itself as: AI-driven workbench for computational materials science — interactive 3D structure viewer, natural-language CatBot assistant, visual DAG workflow engine, HPC job submission… The licence is AGPL-3.0.

When your agent uses it

Tasks that involve Drug discovery and cheminformatics

Example prompts

“/packmol”

Requirements

Compatibility (from SKILL.md): Requires Packmol installed (apt install packmol or compiled from source). Input molecules must be in PDB or XYZ format.

Workflow steps

2 steps, taken from the step headings in SKILL.md.

Prepare molecule files
Create Packmol input and run

What it can do on your machine

Read from SKILL.md and the folder at commit fd6291b. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are bash).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Compatibility
Requires Packmol installed (apt install packmol or compiled from source). Input molecules must be in PDB or XYZ format.
From compatibility in the SKILL.md frontmatter.

Context cost

Packmol loads about 1.1k tokens when it runs. Until then it costs about 47 tokens; SKILL.md has 346 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~47
When it runs · the whole SKILL.md, loaded when a task matches: ~1.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from Hello-QM/catgo-LRG at commit fd6291b, republished under its AGPL-3.0 licence (© Hello-QM). 346 words, ~1,102 tokens.

Download SKILL.mdSave it as .claude/skills/packmol/SKILL.md (or your agent's skills folder).

name: packmol
description: Generate initial configurations for molecular simulations using Packmol. Build liquid boxes, mixtures, solutions, and solvated systems by packing molecules into a defined region.
compatibility: Requires Packmol installed (apt install packmol or compiled from source). Input molecules must be in PDB or XYZ format.
catalog-hidden: true

Packmol — Mixture/Solution Box Generation

When to Use

User needs to build a liquid simulation box (water, organic solvents)
User wants to create a mixture of different molecules
User needs to solvate a solute in a solvent box
User is preparing initial structures for LAMMPS ReaxFF or classical MD
User needs to fill a region with molecules at a target density

Prerequisites

Packmol installed (packmol < /dev/null should print version)
Molecule coordinate files in PDB or XYZ format
For molecules from SMILES: first convert with Open Babel (data/openbabel/SKILL.md)

Workflow Steps

1. Prepare molecule files

If starting from SMILES, convert to PDB first:

bash

obabel -:"O" -O water.pdb --gen3d -h
obabel -:"CCO" -O ethanol.pdb --gen3d -h

2. Create Packmol input and run

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "packmol_mix",
  "command": "packmol < mixture.inp > packmol.log 2>&1",
  "input_files": {
    "mixture.inp": "<packmol input>",
    "water.pdb": "<water coords>",
    "ethanol.pdb": "<ethanol coords>"
  },
  "system_name": "water_ethanol_mix"
})

Packmol Input Template — Simple Liquid Box

tolerance 2.0
filetype pdb
output mixture.pdb

structure water.pdb
  number 1000
  inside box 0.0 0.0 0.0 30.0 30.0 30.0
end structure

Packmol Input Template — Binary Mixture

tolerance 2.0
filetype pdb
output mixture.pdb

# Water (70% by count)
structure water.pdb
  number 700
  inside box 0.0 0.0 0.0 40.0 40.0 40.0
end structure

# Ethanol (30% by count)
structure ethanol.pdb
  number 300
  inside box 0.0 0.0 0.0 40.0 40.0 40.0
end structure

Packmol Input Template — Solvated Solute

tolerance 2.0
filetype pdb
output solvated.pdb

# Solute (fixed at center)
structure solute.pdb
  number 1
  center
  fixed 20.0 20.0 20.0 0.0 0.0 0.0
end structure

# Solvent around solute
structure water.pdb
  number 500
  inside box 0.0 0.0 0.0 40.0 40.0 40.0
  outside sphere 20.0 20.0 20.0 5.0
end structure

Packmol Input Template — Layered System (e.g., Interface)

tolerance 2.0
filetype pdb
output interface.pdb

# Liquid phase
structure hexane.pdb
  number 200
  inside box 0.0 0.0 0.0 30.0 30.0 15.0
end structure

# Gas phase
structure oxygen.pdb
  number 50
  inside box 0.0 0.0 15.0 30.0 30.0 30.0
end structure

Box Size Estimation

Target density determines box size. For water at 1 g/cm3:

N_molecules * M_molecule / (N_A * V_box) = density

For 1000 water molecules:
V = 1000 * 18.015 / (6.022e23 * 1.0) = 2.993e-20 cm3
L = V^(1/3) = 3.1e-7 cm = 31.0 Angstrom

Use a box slightly larger (e.g., 32 Ang) and equilibrate with NPT MD.

Parameter Guidance

Parameter	Typical value	Notes
tolerance	2.0 Ang	Minimum distance between atoms of different molecules
filetype	pdb or xyz	Must match input molecule files
number	varies	Number of molecules of each type
inside box	x0 y0 z0 x1 y1 z1	Rectangular region (Angstrom)
inside sphere	cx cy cz r	Spherical region
outside sphere	cx cy cz r	Exclusion zone (for solvation)
fixed	x y z a b c	Fix position and orientation (angles in degrees)

Common Pitfalls

Tolerance too small — tolerance 2.0 works for most cases. Smaller values cause Packmol to fail to converge.
Box too small — if density is too high, Packmol cannot place all molecules. Increase box size.
Wrong filetype — filetype pdb must match the actual input file format.
No equilibration after Packmol — Packmol output is NOT equilibrated. Always run NPT MD to relax the density.
Missing hydrogens — ensure input molecules have correct hydrogens before packing.
Molecule overlap with solute — use outside sphere to prevent solvent from overlapping with a fixed solute.
Convergence failure — if Packmol does not converge, increase tolerance or box size, or reduce molecule count.

Files

Just SKILL.md in .claude/skills/packmol of Hello-QM/catgo-LRG.

Open the folder on GitHubat commit fd6291b

Compare with similar skills

Packmol next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Packmol compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Packmol this skillHello-QM/catgo-LRG	205	—	~1.1k	Automated safety check: Pass	AGPL-3.0	15 days ago
MolecodeAtomFlow-AI/MoleCode	305	—	~1.9k	Automated safety check: Pass	MIT	4 mo ago
Drug DiscoveryTommy-yw/RunbookHermes	546	1 repos	~2.3k	Automated safety check: Pass	MIT	4 mo ago
DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills	48k	1 repos	~3k	Automated safety check: Notes	MIT	2 days ago
Biomedical Analysis Dispatchxjtulyc/MedgeClaw	617	1 repos	~2k	Automated safety check: Pass	None	6 mo ago
Edu Chem Reactionwy51ai/edulab	1.4k	—	~1.2k	Automated safety check: Pass	Apache-2.0	9 days ago

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Questions about Packmol

What does Packmol do?

Generate initial configurations for molecular simulations using Packmol. Packmol is an agent skill from Hello-QM/catgo-LRG. Generate initial configurations for molecular simulations using Packmol.

When should I use Packmol?

Packmol fits situations like: tasks that involve Drug discovery and cheminformatics.

How do I install Packmol in Claude Code?

Run `npx skills add Hello-QM/catgo-LRG --skill packmol -a claude-code`. Or copy the skill folder (.claude/skills/packmol in Hello-QM/catgo-LRG) into .claude/skills/packmol in your project. Claude Code loads it when a task matches its description.

How do I install Packmol in Codex?

Run `npx skills add Hello-QM/catgo-LRG --skill packmol -a codex`. Or copy the skill folder (.claude/skills/packmol in Hello-QM/catgo-LRG) into .agents/skills/packmol in your project. Codex loads it when a task matches its description.

Can I use Packmol in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add Hello-QM/catgo-LRG --skill packmol -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/packmol, .gemini/skills/packmol, .github/skills/packmol and .opencode/skills/packmol in your project.

What does Packmol need to run?

SKILL.md names no scripts, command-line tools or credentials: Packmol is instructions for the agent only. Compatibility (from SKILL.md): Requires Packmol installed (apt install packmol or compiled from source). Input molecules must be in PDB or XYZ format. .

Does Packmol access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Packmol safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Packmol use?

Packmol is published under the AGPL-3.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Packmol use?

About 1.1k tokens (SKILL.md is roughly 4.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Packmol?

Skills that share tags, products or a category with Packmol: Molecode (AtomFlow-AI/MoleCode, 305 stars), Drug Discovery (Tommy-yw/RunbookHermes, 546 stars), DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars) and Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Packmol?

Hello-QM (a GitHub user) maintains it in Hello-QM/catgo-LRG, which has 205 GitHub stars. The repository holds 75 skills in this directory. The repository was last updated on September 22, 2026.

Source: Hello-QM/catgo-LRG on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Packmol

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Compatibility

Context cost

Safety

SKILL.md

Packmol — Mixture/Solution Box Generation

When to Use

Prerequisites

Workflow Steps

1. Prepare molecule files

2. Create Packmol input and run

Packmol Input Template — Simple Liquid Box

Packmol Input Template — Binary Mixture

Packmol Input Template — Solvated Solute

Packmol Input Template — Layered System (e.g., Interface)

Box Size Estimation

Parameter Guidance

Common Pitfalls

Files

Compare with similar skills

Similar skills

More from Hello-QM/catgo-LRG

Related

Questions about Packmol