Antechamber

What it does

Example prompts

• “/antechamber”

Requirements

• Compatibility (from SKILL.md): Requires AmberTools installed (conda install -c conda-forge ambertools). antechamber, parmchk2, and tleap must be in PATH.

Workflow steps

3 steps, taken from the first numbered list in SKILL.md.

1. 1AmberTools installed (antechamber --help)
2. 2Input molecule structure (mol2, pdb, or Gaussian output for RESP)
3. 3For RESP charges: Gaussian output with pop=mk iop(6/33=2) ESP data

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 AmberTools installed (conda install -c conda-forge ambertools). antechamber, parmchk2, and tleap must be in PATH.

  From compatibility in the SKILL.md frontmatter.

Context cost

Antechamber loads about 1.1k tokens when it runs. Until then it costs about 49 tokens; SKILL.md has 279 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~49

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

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). 279 words, ~1,138 tokens.

name

antechamber

description

Use AmberTools antechamber for molecular force field parameterization. Generates GAFF/GAFF2 parameters and AM1-BCC or RESP charges for use in AMBER or LAMMPS classical MD simulations.

compatibility

Requires AmberTools installed (conda install -c conda-forge ambertools). antechamber, parmchk2, and tleap must be in PATH.

catalog-hidden

true

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "antechamber_param",
  "command": "bash parameterize.sh",
  "input_files": {
    "parameterize.sh": "<script content>",
    "molecule.pdb": "<molecule structure>"
  },
  "system_name": "ligand_param"
})

#!/bin/bash
set -e

# Step 1: Assign GAFF2 atom types and AM1-BCC charges
antechamber -i molecule.pdb -fi pdb \
            -o molecule.mol2 -fo mol2 \
            -c bcc -at gaff2 \
            -nc 0 -m 1 \
            -rn LIG

# Step 2: Check for missing parameters
parmchk2 -i molecule.mol2 -f mol2 \
         -o molecule.frcmod -a Y

# Step 3: Build topology with tleap
cat > tleap.in << 'EOF'
source leaprc.gaff2
LIG = loadmol2 molecule.mol2
loadamberparams molecule.frcmod
check LIG
saveamberparm LIG molecule.prmtop molecule.inpcrd
savemol2 LIG molecule_leap.mol2 1
quit
EOF

tleap -f tleap.in > tleap.log 2>&1
echo "Generated: molecule.prmtop molecule.inpcrd"

#!/bin/bash
set -e

# Step 1: Generate Gaussian input for ESP
antechamber -i molecule.pdb -fi pdb \
            -o molecule.gjf -fo gcrt \
            -gm "%mem=4GB" -gn "%nproc=8" \
            -ge "molecule.gesp" \
            -gk "#HF/6-31G* opt pop=mk iop(6/33=2)"

# Step 2: Run Gaussian (separate task)
# g16 molecule.gjf

# Step 3: Extract RESP charges from Gaussian output
antechamber -i molecule.log -fi gout \
            -o molecule.mol2 -fo mol2 \
            -c resp -at gaff2 \
            -nc 0 -m 1 -rn LIG

# Step 4: Check and build topology (same as AM1-BCC)
parmchk2 -i molecule.mol2 -f mol2 -o molecule.frcmod -a Y

cat > tleap.in << 'EOF'
source leaprc.gaff2
LIG = loadmol2 molecule.mol2
loadamberparams molecule.frcmod
check LIG
saveamberparm LIG molecule.prmtop molecule.inpcrd
quit
EOF

tleap -f tleap.in > tleap.log 2>&1

source leaprc.water.tip3p
LIG = loadmol2 molecule.mol2
loadamberparams molecule.frcmod
solvateBox LIG TIP3PBOX 12.0
addIonsRand LIG Na+ 0 Cl- 0   # Neutralize
saveamberparm LIG solvated.prmtop solvated.inpcrd
quit

© Hello-QM, AGPL-3.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

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

Open the folder on GitHubat commit fd6291b

Used in 1 other repository

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in Hello-QM/catgo-LRG, which our catalogue first saw on October 7, 2026.

• majiayu000/claude-skill-registryskills/bash/antechamber