Gaussian QM Fragmentation and 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 fragments molecules around each rotatable bond and then performs a torsion scan on each fragment. Fragments are created around rotatable bonds to allow torsion scans to mimic the energetics of that torsion in the original molecule.
Torsion 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 rotating torsion in each fragment. Then a QM optimization is performed with the torsion constrained while all other degrees of freedom are relaxed.
Finally, these torsion scans are used to determine the torsion rules
that should be used for each rotatable bond in future conformer generation.
There are two outputs from this floe:
First, the fragments as multiconformer molecules where each
conformer represents one angle from the torsion scan.
Second, the input (parent) molecules with the torsion rules for conformer generation.
The parent output can be used as input for the Gaussian QM Conformer Ensemble
Floe and the custom torsion rules will be
used in the conformer generation step.
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 Rules Output (out): Output dataset to write to
Required
Type: dataset_out
Default: gau_torsion_rule_output
Output Dataset (failure): Dataset to store records which fail during the floe.
Required
Type: dataset_out
Default: gaussian_fragmentation_failures
Output Dataset (fragment_output): Dataset to store fragment records with torsion scans. Each record is a multiconformer molecule with one conformer per angle sampled.
Required
Type: dataset_out
Default: gau_fragment_output
Gaussian Fragmentation Report Title (frag_floe_report_name):
Type: string
Default: Fragmentation_Report
Backup Collection Name (collection_name): Name of collection to store backup checkpoint files.
Type: collection_sink
Default: Gaussian Backup Collection
Torsion Scan Parameters
Torsion Increment (resolution): Torsion increment angle in degrees for the scan.
Type: decimal
Default: 5
QM Switch (qm_switch): Controls QM calculation. When On, a QM optimization is run on each fragment for each torsion. When Off, the force field energies are used for rule generation (recommended only for testing).
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 Parameters
Gaussian Energy Field (energy_field): New field created on torsion scan output to store QM energy at each torsion angle.
Required
Type: field_parameter::float
Default: Gaussian Energy (kcal/mol)
Gaussian Strain Energy Field (gau_strain_energy): New field created on torsion scan output to store relative QM energies at each torsion angle for each fragment.
Required
Type: field_parameter::float
Default: Gaussian Strain Energy (kcal/mol)
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
Remove Extended Ring Atoms (remove_extended): When On, heuristics are used to reduce the size of the fragments by removing atoms from extended ring systems where possible. Turn Off to keep all atoms in complex ring systems. In very rare cases, for molecules with obscure chemistries, turning this Off may reduce problems in fragmentation.
Type: boolean
Default: True
Choices: [True, False]
Energy Cutoff (max_sample_energy): Energy cutoff for choosing angles in custom torsion rules. Default value of 5 kcal is chosen based on the assumption that these rules will later be used to generate conformers in a 10 kcal/mol energy window. If you plan to generate a QM conformer ensemble in a larger energy window you may want to increase this cutoff accordingly.
Type: decimal
Default: 5
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
Advanced Force Field Parameters
Force Field (ff_type): Built-in force field model to be used.
Type: string
Default: mmff94s
Choices: [‘mmff94s’, ‘parsley’, ‘sage’]
None (ff_solvent_model): Solvent model to be used
Type: string
Default: Sheffield
Choices: [‘Gas-phase’, ‘Sheffield’, ‘SheffieldPB’]
Penalty Force Constant (force_constant): Force constant used to apply the dihedral constraint.
Type: decimal
Default: 100000
Conformer Energy Field 2 (ff_en_field): Energy field for force field energies.
Type: field_parameter::float
Default: FF Energy (kcal/mol)
Conformer Strain Energy Field 2 (ff_strain_field):
Type: field_parameter::float
Default: Relative FF Energy (kcal/mol)