Gaussian 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/Gaussian
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 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)
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
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
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: 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)
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
Backup Collection Name (collection_name): Name of collection to store backup checkpoint files.
Type: collection_sink
Default: Gaussian Backup Collection
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]