Psi4 QM SMARTS Torsion Scan
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Solution-based/Small Molecule Lead-opt/QM Analysis/Torsions & Strain
Task-based/Quantum Mechanics/Torsion Sampling
Role-based/Computational Chemist
Product-based/Quantum Mechanics/Psi4
Description
This floe performs a 1-D torsion energy scan on a torsion where the atoms are specified with a SMARTS substructure pattern.
Scanning is performed with the OETorsionScan function from OESzybki TK at a specified resolution (in degrees). This function includes a force field minimization of all internal degrees of freedom except for the selected torsion.
An optional QM calculation is performed with Psi4, either an optimization (Optimization Switch=True) or a single point energy (SPE) calculation (Optimization Switch=False). In the case of the QM optimization, the torsion is constrained and all other degrees of freedom are relaxed further.
The output of this floe is a multiconformer molecule for each input molecule, where each conformer represents one angle from the torsion scan.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Input Dataset (in): The dataset(s) to read records from
Required
Type: data_source
Outputs
Psi4 Torsion Scan Output (out): Dataset to store torsion scan output records.
Required
Type: dataset_out
Default: psi4_torscan_output
Failure Output (failure): Dataset to store records which fail during this floe.
Required
Type: dataset_out
Default: psi4_torscan_failures
Floe Report Name (tors_report_name): Title for the torsion scan floe report.
Type: string
Default: Psi4 Torsion Scan Report
Torsion Scan Parameters
SMARTS Pattern (smarts): The string that defines the substructure as a SMARTS.
Required
Type: string
Default: [!#1]~[!#1]-!@[!#1]~[!#1]
Torsion Increment (resolution): Torsion angle increment in degrees
Type: decimal
Default: 5.0
QM Switch (QM_switch): When turned On, a QM calculation is performed; either single point energy or optimization is set with the Optimization Switch parameter. When turned Off, only the force field energies are reported for each torsion scan.
Required
Type: boolean
Default: True
Choices: [True, False]
Optimization Switch (adiabatic_switch): When turned On, a geometry optimization is performed constraining only the scanned torsion. When turned Off, a single point energy calculation is performed on the force field optimized conformers.
Required
Type: boolean
Default: True
Choices: [True, False]
Psi4 Calculation Parameters
Psi4 Hamiltonian (psi4_method): Hamiltonian used for geometry optimization or single point energy calculation.
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 (psi4_basis): Basis set used for geometry optimization or single point energy calculation.
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 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 GeomeTRIC
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 Force Field Parameters
Force Field (ff_type): Built-in force field model to be used.
Type: string
Default: sage
Choices: [‘mmff94s’, ‘parsley’, ‘sage’]
Penalty Force Constant (force_constant): Force constant used to apply the dihedral constraint.
Type: decimal
Default: 100000
None (solvent_model): Solvent model to be used
Type: string
Default: Gas-phase
Choices: [‘Gas-phase’, ‘Sheffield’, ‘SheffieldPB’]
Force Field Energy Field (ff_en_field): Name of field for storing force field energies.
Type: field_parameter::float
Default: FF Energy (kcal/mol)