Psi4 QM SMARTS Torsion Scan

Category Paths

  • 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

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 the OESzybki Toolkit at a specified resolution (in degrees). This function includes a force field minimization of all internal degrees of freedom except for the selected torsion.

Then, 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 multi-conformer 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 as 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 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’, ‘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’, ‘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

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