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)
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
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
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)