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): RMS threshold for duplicate conformer 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