qp.manager.create.create_jobs

qp.manager.create.create_jobs(pdb_list_path, output_dir, optimization, basis, method, guess, use_charge_embedding, charge_embedding_cutoff, charge_embedding_charges, gpus, memory, scheduler, pcm_radii_file, dielectric, use_implicit_solvent=True)[source]

Generate QM job input files for all extracted clusters.

Creates TeraChem input files (qmscript.in) and scheduler submission scripts (jobscript.sh) for each cluster directory. Automatically determines charge and spin multiplicity from the input CSV and charge.csv files.

Parameters:

  • pdb_list_path (str) – Path to the input CSV with pdb_id, oxidation, multiplicity.

  • output_dir (str) – Base output directory containing PDB subdirectories.

  • optimization (bool) – If True, run geometry optimization; otherwise single-point energy.

  • basis (str) – Basis set name (e.g., 'lacvps_ecp').

  • method (str) – DFT method/functional (e.g., 'wpbeh').

  • guess (str) – Initial wavefunction guess method (e.g., 'generate').

  • use_charge_embedding (bool) – If True, generate point charge embedding file.

  • charge_embedding_cutoff (float) – Distance cutoff in angstroms for MM point charges.

  • charge_embedding_charges (str or None) – Path to a JSON file with custom partial charges. When None, the built-in AMBER ff14SB charges are used.

  • gpus (int) – Number of GPUs to request.

  • memory (str) – Memory allocation string (e.g., '8G').

  • scheduler (str) – Job scheduler type ('slurm' or 'sge').

  • pcm_radii_file (str) – Path to PCM radii file for implicit solvent.

  • dielectric (float) – Dielectric constant for PCM solvent model.

  • use_implicit_solvent (bool, optional) – If True, include PCM implicit solvent in TeraChem input. Can be enabled alongside use_charge_embedding. Default is True.