Psi4 QM Tautomer Floe

Category Paths

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

  • Solution-based/Small Molecule Lead-opt/QM Analysis/Tautomer Analysis

  • Task-based/Quantum Mechanics/Energetic Analysis

  • Role-based/Computational Chemist

  • Product-based/Quantum Mechanics/Psi4

Description

This floe begins by enumerating all reasonable tautomers of the input molecules. Then it performs a local minimum search by (1) generating conformers, (2) performing a geometry optimization, and (3) deduplicating local minima. The last step is an optional single point energy calculation at a higher level of theory. The final output includes one record for each enumerated tautomer as a multiconformer molecule. The minimum energy for each tautomer is saved on the primary molecule record, and a report is created summarizing the energy distributions for each tautomer.

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 (confs_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

Optimized Tautomer Output (out): Dataset to store optimized conformers of each tautomer. There is one multiconformer record for each enumerated tautomer.

  • Required

  • Type: dataset_out

  • Default: psi4_tautomer_opt_out

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

  • Required

  • Type: dataset_out

  • Default: psi4_tautomer_failures

Tautomer Floe Report Title (taut_floe_report_name):

  • Type: string

  • Default: Psi4 Tautomer Floe Report

Tautomer and 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

Conformer Energy Window (conf_en_window): Energy window for conformer selection

  • Type: decimal

  • Default: 50.0

Include Single Point Energy (spe_switch): Optionally perform an additional single point energy calculation (On). Otherwise, only the final energy for the geometry optimization is stored (Off). If On, make sure that the single point energy method and basis set are different from the geometry optimization.

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Generate Reasonable Tautomers Only (reasonable_tautomers): Choice of whether to generate reasonable tautomers (On) or all possible tautomers (Off).

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Strict Stereo (strict_stereo): Flag indicating if all chiral atoms and bonds must have specified stereochemistry during conformer generation. If atoms and bonds in the input molecule have their stereochemistry specified, that stereochemistry will remain fixed during tautomer enumeration. However, depending on the molecule, generated tautomers may have unspecified stereochemistry. Those tautomers will fail if this is set to On.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Psi4 Calculation Parameters

Psi4 Hamiltonian (Geometry Optimization) (psi4_gopt_method): Method used for Psi4 geometry optimization.

  • 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.

  • 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’]

Psi4 Hamiltonian (Single Point Energy) (psi4_spe_method): Method used for optional 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 optional 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

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’]

Advanced Parameters

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