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Skills for QM cluster model extraction and ONIOM calculation setup from protein-ligand PDB files.
npx claudepluginhub william-dawson/oniom-skillsQM cluster model extraction and ONIOM calculation setup from protein-ligand PDB files. Includes three skills: cluster extraction with PyMOL, ONIOM input generation for XTB/ORCA, and SLURM batch script preparation. Requires PyMOL on $PATH; XTB and ORCA optional.
A Claude Code plugin for setting up QM and QM/MM calculations from protein-ligand PDB files. The protein file you are working on should be in CHARMM format (generate with CHARMM-GUI)
/plugin marketplace add william-dawson/oniom-skills
/plugin marketplace update oniom-skills
/plugin install pymol@oniom-skills
/reload-plugins
This plugin provides three skills that guide you through the full workflow from raw PDB to a running calculation on your cluster:
/pymol:pymol — Extract a QM cluster model. Normalizes CHARMM PDBs, identifies the ligand, selects residues within a cutoff, applies amide capping, handles metal coordination shells, and determines the cluster charge.
/pymol:oniom — Set up a two-layer ONIOM calculation. Three approaches: XTB built-in ONIOM, 3-point manual (three separate calculations you control), or ORCA native QM/XTB. Walks you through method, cutoff, charge, and multiplicity one question at a time.
/pymol:slurm — Generate a SLURM batch script. Asks about partition, account, CPUs, memory, wall time, and how your software is installed (module, conda, or custom path). Produces a ready-to-submit script.
The skills are conversational — they inspect your structure, ask about ambiguous chemistry (ligand charge, protonation states, metal oxidation states, open-shell character), and write scripts tailored to your specific system.
$PATHSay something like:
Using your pymol skills, prepare an oniom calculation with XTB on the pdb file in this directory
You can install these skills directly into Codex from GitHub.
For a project-local install:
mkdir -p .codex/skills
python3 ~/.codex/skills/.system/skill-installer/scripts/install-skill-from-github.py \
--repo william-dawson/oniom-skills \
--path skills/pymol skills/oniom skills/slurm \
--dest "$PWD/.codex/skills"
PyMOL is developed by Schrödinger, LLC. XTB is developed by the Grimme group. ORCA is developed by the Neese group. This plugin provides only the Claude Code skill layer on top of these tools.