claude

pymol

Extract QM cluster models and set up ONIOM calculations from protein-ligand PDB files. Requires PyMOL, XTB (≥6.6), and optionally ORCA.

1 on GitHubby william-dawsonv0.6.0MITupdated 3 months ago
/

Plugin pymol from marketplace oniom-skills in william-dawson/oniom-skills. Commands read from the repo's manifest — 1 month ago.

What it installs

Skills (3)

  • oniom

    Set up a two-layer ONIOM calculation using XTB or ORCA. Guides method, charge, multiplicity, and inner region decisions. Use after running the pymol skill.

  • pymol

    Extract a QM cluster model from a protein-ligand PDB file. Guides ligand identification, residue selection, amide capping, and charge determination. Use when preparing a cluster for QM or QM/MM calculations.

  • slurm

    Generate SLURM batch scripts for HPC job submission. Ask the user about partition, resources, and software environment one question at a time.

View source on GitHub

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