Gaussian 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/Gaussian

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 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 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

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

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

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]

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

Instance Type (gaussian_instance_type): ADVANCED: This parameter is to specify the specific AWS instance type for the Gaussian calculation to run on. Orion has a scheduler which will automatically find the best instance for the other hardware requirements. You should not specify this parameter unless you are absolutely sure you want to limit instance type. Since Gaussian Calculations are performed on many serial Cubes this parameter is promoted to make sure it is set on all of the copies of the Gaussian calculation Cube.

  • Type: string

Update Field Names

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