Gaussian QM UI 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/Gaussian

Description

This floe performs a 1-D torsion energy scan on a torsion where the atoms are selected with the 2D Viewer.

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 Gaussian, 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

Select Torsion Input (ui_result): Select an existing molecule or sketch a new one. Then, use the Sketcher to select the atoms for this torsion scan.

  • Required

  • Type: fragment_input

Reference Dataset (Optional) (ref_input): Reference molecules will be used to compare reference torsions to the scan of the torsion indicated in the sketched molecule above.

  • Type: data_source

Outputs

Gaussian Torsion Scan Output (out): Dataset to store torsion scan output records.

  • Required

  • Type: dataset_out

  • Default: gau_torscan_output

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

  • Required

  • Type: dataset_out

  • Default: gau_torscan_failures

Floe Report Name (tors_report_name): Title for the torsion scan floe report

  • Type: string

  • Default: Gaussian Torsion Scan Report

Torsion Scan Parameters

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]

Gaussian Calculation Parameters

Gaussian Solvent Environment (solvent): Solvent environment used for this Gaussian calculation

  • Type: string

  • Default: Gas Phase

  • Choices: [‘Gas Phase’, ‘Water IEFPCM’, ‘Water CPCM’, ‘Water SMD’, ‘DMSO IEFPCM’, ‘DMSO CPCM’, ‘DMSO SMD’, ‘Octanol IEFPCM’, ‘Octanol CPCM’, ‘Octanol SMD’]

Gaussian Method (method): Method used for this Gaussian calculation

  • Type: string

  • Default: HF

  • Choices: [‘HF’, ‘B3LYP’, ‘B3LYP - GD3’, ‘B3LYP - GD3BJ’, ‘B2PLYP’, ‘B2PLYPD3’, ‘M06’, ‘M062X’, ‘M06L’, ‘MN15’, ‘MN15L’, ‘PW6B95D3’, ‘CAM-B3LYP’, ‘CAM-B3LYP - GD3’, ‘CAM-B3LYP - GD3BJ’, ‘WB97X’, ‘wB97XD’, ‘LC-wHPBE’, ‘PBE1PBE’, ‘MP2’, ‘PW91PW91’, ‘PM6’]

Gaussian Basis Set (basis): Basis set used for property calculation with Gaussian

  • Type: string

  • Default: 6-31G

  • Choices: [‘3-21G’, ‘6-31G’, ‘6-31G*’, ‘6-31+G*’, ‘6-31G**’, ‘6-31+G**’, ‘6-311G**’, ‘6-311+G**’, ‘6-311G(2d,2p)’, ‘def2SVP’, ‘def2TZVP’, ‘def2TZVPP’, ‘aug-cc-pvdz’, ‘aug-cc-pvtz’, ‘’]

Hardware Requirements for Gaussian Calculation

Gaussian # Threads (gaussian_nthreads): Number of CPUs for Gaussian calculation.

  • Type: integer

  • Default: 8

Gaussian Memory (gaussian_memory): Memory for Gaussian calculations in MBs.

  • Type: decimal

  • Default: 14400

Gaussian Disk Space (gaussian_disk_space): Temporary disk space (in MB) required for your calculation.

  • Type: decimal

  • Default: 25600

Advanced

Gaussian Energy Field (energy_field): Field created during Floes to store Gaussian Energy

  • Type: field_parameter::float

  • Default: Gaussian Energy (kcal/mol)

Conformer Angle Field (angle_field):

  • Type: field_parameter::float

  • Default: Torsion angle

Timeout for Gaussian Calculation (Hours) (gau_timeout): Parallel Cubes have a strict time limit, this parameter stops the gaussian calculation before it reaches that limit. Note, this is a maximum only, the cube will finish when the calculation finishes if it is less than the time limit.

  • Type: decimal

  • Default: 10

Maximum number of retries (gau_retries): Maximum number of attempts to perform QM calculation

  • Type: integer

  • Default: 3

Save Log files (store_log_file): Save output log files for all calculations, they are always saved for failed calculations.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Report Name for Log Files (gau_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: Gaussian Log File Report

Advanced Force Field Parameters

Force Field (ff_type): Built-in force field model to be used.

  • Type: string

  • Default: sage_openff200

  • Choices: [‘mmff94s’, ‘smirnoff99frost’, ‘parsley_openff100’, ‘parsley_openff111’, ‘parsley_openff121’, ‘parsley_openff131’, ‘sage_openff200’]

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: Sheffield

  • Choices: [‘Gas-phase’, ‘Sheffield’, ‘SheffieldPB’]

Conformer Energy Field 1 (ff_en_field): Energy field for force field energies.

  • Required

  • Type: field_parameter::float

  • Default: FF Energy (kcal/mol)