Psi4 Combined Tautomer and Torsion Sampling Conformer Floe

Conformation generation Floe with sampling tautomers and torsions.

Promoted Parameters

  • reasonable_tautomers (boolean) : Choice of rather to generate reasonable tautomers (On) or all possible tautomers (Off).
    Default: True
  • conf_strain_energy_field (Field Type: Float) : Field to store the relative QM energy after the single point energy calculation.
    Default: Psi4 Strain Energy (kcal/mol)
  • gopt_energy_field (Field Type: Float) : Field to store the absolute QM energy at the end of the conformer optimization.
    Default: Psi4 Opt Energies (kcal/mol)
  • confgen_rmsd_threshold (decimal) : RMSD threshold for conformer duplicate removal
    Default: 0.75 Max: 5.0
  • test_rmsd2 (decimal) : RMSD threshold for conformer duplicate removal
    Default: 0.5 Max: 5.0
  • test_rmsd3 (decimal) : RMSD threshold for conformer duplicate removal
    Default: 0.25 Max: 5.0
  • frag_floe_report_name (string) :
    Default: taut_torsion_conf_report
  • failure (dataset_out) : Dataset to store records which fail during this Floe.
    Default: psi4_fragmentation_failures
  • frag_out (dataset_out) : Dataset to store fragment records with torsion scans.
    Default: fragment_output
  • in (data_source) : The dataset(s) to read records from
  • limit_confs (integer) : This parameter limits the number of conformers optimized, to prevent accidentally spending more than expected on a single Floe. If more than this number of conformers are generated, then only one conformer will be optimized to learn about the cost of this floe/conformer. If the max number of conformers is set to 0, then ALL generated conformers are optimized.
    Default: 100
  • psi4_energy_window (decimal) : Psi4 energy window for filtering high strain conformers. When the filter is set to -1 all conformers are included in output.
    Default: 10.0
  • conf_energy_field (Field Type: Float) : Field to store the absolute QM energy of each conformer after the single point energy calculation.
    Default: Psi4 Energy (kcal/mol)
  • psi4_gopt_data_out (dataset_out) : Dataset to store optimized conformers in the specified energy window, each record has a single conformer.
    Default: confs_psi4_gopt_spe
  • psi4_spe_method (string) : Method used for single point energy calculation.
    Default: B3LYP-D3MBJ
    Choices: HF3c, PBEh3c, HF, HF-D3, B3LYP, B3LYP-D3BJ, B3LYP-D3MBJ, B2PLYP-D3BJ, M06, M06-2X, M06-L, MN15-D3BJ, MN15-L, PW6B95-D3BJ, CAM-B3LYP, CAM-B3LYP-D3BJ, WB97X, WB97X-D, WB97X-V, PBE, PBE0
  • psi4_spe_basis (string) : Basis set used for single point energy calculation.
    Default: 6-31G*
    Choices: :green:``, minix, 6-31G, 6-31G*, 6-31+G*, 6-31G**, 6-31+G**, 6-311G**, 6-311+G**, 6-311G(2d,2p), def2-SVP, def2-SVPD, def2-TZVP, def2-TZVPD, def2-TZVPP, def2-TZVPPD, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, aug-cc-pVTZ, LanL2DZ
  • psi4_memory (decimal) : Memory for Psi4 calculations in MBs
    Default: 14400 Min: 256.0 Max: 8589934592
  • psi4_nthreads (integer) : Number of CPUs for Psi4 calculations
    Default: 8 Min: 1 Max: 128
  • psi4_gopt_method (string) : Method used for Psi4 geometry optimization.
    Default: HF3c
    Choices: HF3c, PBEh3c, HF, HF-D3, B3LYP, B3LYP-D3BJ, B3LYP-D3MBJ, B2PLYP-D3BJ, M06, M06-2X, M06-L, MN15-D3BJ, MN15-L, PW6B95-D3BJ, CAM-B3LYP, CAM-B3LYP-D3BJ, WB97X, WB97X-D, WB97X-V, PBE, PBE0
  • psi4_gopt_basis (string) : Basis set for Psi4 geometry optimization. Default empty basis set (‘’) goes with HF3c which has one built in.
    Default: “”
    Choices: :green:``, minix, 6-31G, 6-31G*, 6-31+G*, 6-31G**, 6-31+G**, 6-311G**, 6-311+G**, 6-311G(2d,2p), def2-SVP, def2-SVPD, def2-TZVP, def2-TZVPD, def2-TZVPP, def2-TZVPPD, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, aug-cc-pVTZ, LanL2DZ
  • constrain_polar_hydrogens (boolean) : Torsions terminating in a polar hydrogen (i.e. hydroxyl groups) will be constrained along with all other rotatable bonds (On). Otherwise (Off), only rotatable bonds with heavy atoms will be constrained.
    Default: True
  • confgen_data_out (dataset_out) : Dataset to store QM optimized conformers before deduplication. If a job is cancelled early (either by the user or hitting a cost threshold is reached), these intermediate optimized conformers, will still be saved.
    Default: all_conf_gopt
  • out (dataset_out) : Dataset to store records with custom torsion rules, these can be used as input in ‘Psi4 QM Conformer Ensemble’ or Psi4 QM Local Minima Search’ Floes to use the custom torsion rules during conformer generation.
    Default: torsion_rule_output

Extra Required Parameters

  • Individual Molecules Switch (boolean) : Output tautomers as individual molecules on the primary output molecule
    Default: True
  • atom tag (string) : Tag for the atoms in torsion
  • Switch (boolean) : This parameter controls whether records are sent to the ‘true’ or ‘false’ port
    Default: True
  • Psi4 Energy Field (Field Type: Float) : New field created on torsion scan output to store QM energy at each torsion angle.
    Default: Psi4 Energy (kcal/mol)
  • Hit List Size (integer) : The desired size of the hit list.
    Default: 1 Min: 1