Psi4 QM Conformer Ensemble

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Solution-based/Small Molecule Lead-opt/QM Analysis/Internal Energies

  • Role-based/Computational Chemist

  • Task-based/Quantum Mechanics/Energetic Analysis

  • Product-based/Quantum Mechanics/Psi4

Description

This floe generates all low-energy conformers of the input molecule. A large ensemble of potential conformations are generated using OpenEye toolkits, through exhaustive sampling of ring conformations, torsions, and hydrogens. To customize torsion rules used for this conformer generation, use output from the Psi4 QM Fragmentation and Torsion Scanning floe.

The generated conformers are optimized using Psi4 at a low level of QM theory with all torsions constrained. The conformers are filtered to remove exact duplicates. Next, the energies are corrected to a higher level of QM theory through a single-point energy calculation. Last, high-strain conformations are removed at the specified energy cutoff.

Conformers are generated for the input molecule; thus, if the primary molecule has multiple conformers, they are ignored. Input molecules with unspecified stereochemistry will fail this floe. The sketcher can be used to draw input molecules where the stereochemistry can be adjusted.

This floe assumes that all input molecules are a part of the same ensemble. Since conformers are generated at the beginning, there is no reason to provide more than one input molecule. However, this floe will also work with multiple tautomers of the same molecule, if they are provided as input. The energy window is applied across all input molecules.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input Dataset (in): The dataset(s) to read records from

  • Required

  • Type: data_source

Outputs

Intermediate Optimization Output (confgen_data_out): Dataset to store QM optimized conformers before deduplication. If a job is cancelled early (either by the user or because a cost threshold is reached), these intermediate optimized conformers will still be saved.

  • Required

  • Type: dataset_out

  • Default: psi4_all_conf_gopt

Psi4 Conformer Ensemble Output (psi4_gopt_data_out): Dataset to store optimized conformers in the specified energy window. Each record has a single conformer.

  • Required

  • Type: dataset_out

  • Default: psi4_confs_gopt_spe

Failure Output (failure): Dataset to store records which fail during this floe.

  • Required

  • Type: dataset_out

  • Default: psi4_conf_ens_failures

Conformer Floe Report Name (conf_report_name): Floe report title that summarizes conformer ensemble results.

  • Type: string

  • Default: Psi4 Conformer Report

Conformer Parameters

RMSD Threshold for Conformer Generation (confgen_rmsd_threshold): RMSD threshold for conformer duplicate removal

  • Type: decimal

  • Default: 0.5

Maximum Conformers (omega_max_confs): Set the maximum conformers to be generated with Omega. Note the more conformers the more expensive the QM optimizations will be.

  • Type: integer

  • Default: 100

Omega Energy Window (conf_en_window): Energy window used for conformer generation in Omega

  • Type: decimal

  • Default: 50.0

Psi4 Energy Window (kcal/mol) (psi4_energy_window): Psi4 energy window for filtering high strain conformers. When the filter is set to -1, all conformers are included in output.

  • Type: decimal

  • Default: 10.0

Psi4 Calculation Parameters

Psi4 Hamiltonian (Geometry Optimization) (psi4_gopt_method): Method used for Psi4 geometry optimization. Remember, geometry optimizations in this floe are performed with all torsions constrained allowing bonds and angles to relax. This may affect which method you chose.

  • Type: string

  • 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’, ‘WB97M-D3BJ’, ‘B97M-D3BJ’, ‘PBE’, ‘PBE0’]

Psi4 Basis Set (Geometry Optimization) (psi4_gopt_basis): Basis set for Psi4 geometry optimization. Default empty basis set (‘’) goes with HF3c, which has one built in. Remember, geometry optimizations in this floe are performed with all torsions constrained allowing bonds and angles to relax. This may affect which method you chose.

  • Type: string

  • Default:

  • Choices: [‘’, ‘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’, ‘DZVP’, ‘cc-pVDZ’, ‘aug-cc-pVDZ’, ‘cc-pVTZ’, ‘aug-cc-pVTZ’, ‘LanL2DZ’]

Optimization Engine (psi4_engine): Chose an engine for the geometry optimization. Psi4

supports both OptKing and GeomeTRIC.

  • Type: string

  • Default: Psi4 OptKing

  • Choices: [‘Psi4 OptKing’, ‘Psi4 GeomeTRIC’]

Psi4 Hamiltonian (Single Point Energy) (psi4_spe_method): Method used for single point energy calculation.

  • Type: string

  • 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’, ‘WB97M-D3BJ’, ‘B97M-D3BJ’, ‘PBE’, ‘PBE0’]

Psi4 Basis Set (Single Point Energy) (psi4_spe_basis): Basis set used for single point energy calculation.

  • Type: string

  • Default: 6-31G*

  • Choices: [‘’, ‘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’, ‘DZVP’, ‘cc-pVDZ’, ‘aug-cc-pVDZ’, ‘cc-pVTZ’, ‘aug-cc-pVTZ’, ‘LanL2DZ’]

Psi4 Memory (psi4_memory): Memory for Psi4 calculations in MBs.

  • Type: decimal

  • Default: 14400

Psi4 #Threads (psi4_nthreads): Number of CPUs for Psi4 calculations.

  • Type: integer

  • Default: 8

Advanced Parameters

Psi4 Optimization Energy Field (psi4_optimize_energy_field): Field containing Psi4 energy from geometry optimization.

  • Type: field_parameter::float

  • Default: Psi4 Opt Energies (kcal/mol)

Psi4 Single Point Energy Field (psi4_energy_field): Field containing Psi4 energy.

  • Type: field_parameter::float

  • Default: Psi4 Energy (kcal/mol)

Psi4 Strain Energy Field (psi4_strain_energy_field): Field to store Psi4 strain energy.

  • Required

  • Type: field_parameter::float

  • Default: Psi4 Strain Energy (kcal/mol)

Save Psi4 Log File (store_log_file): The log file generated from Psi4 is saved. It will be available as a floe report when the floe is complete.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Report Name for Log Files (qm_log_report_name): Floe report to store QM log files. This report is only created if the calculation log files were stored.

  • Type: string

  • Default: Psi4 Log File Report

Advanced Conformer Generation Options

Switch (csp_conf_switch): Use the extra dense conformer generation developed for OpenEye’s

crystal structure prediction protocol. In this algorithm, all fragment enumeration is maintained during deduplication.

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Maximum Conformers for Geometry Optimization (limit_confs): 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 maximum number of conformers is set to 0, then ALL generated conformers are optimized.

  • Type: integer

  • Default: 100

Constrain Torsions with Polar Hydrogens (constrain_polar_hydrogens): Torsions terminating in a polar hydrogen (for example, hydroxyl groups) will be constrained along with all other rotatable bonds (On). Otherwise, only rotatable bonds with heavy atoms will be constrained (Off).

  • Type: boolean

  • Default: True

  • Choices: [True, False]