Gaussian QM Conformer Ensemble
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Solution-based/Small Molecule Lead-opt/QM Analysis
Product-based/Quantum Mechanics/Gaussian
Task-based/Quantum Mechanics/Energetic Analysis
Role-based/Computational Chemist
Description
This floe generates low-energy conformers of the input molecule. Conformers are generated and then a geometry optimization is performed with Gaussian followed by a single-point energy calculation.
A large ensemble of potential conformations are generated using OpenEye toolkits,
through exhaustive sampling of ring conformations, torsions, and hydrogens.
To customize torsion rules used for this conformer generation, use output from the
Gaussian QM Fragmentation and Torsion Scanning Floe.
Next, the generated conformers are optimized using Gaussian at a low level of QM theory. By default, optimizations are performed with all torsions constrained. To perform full geometry optimizations instead, turn the Constrain Torsions Off. The conformers are filtered to remove exact duplicates. Next, the energies are corrected to a higher level of QM theory through a single-point energy calculation. Last, high-strain conformations are removed at the specified energy cutoff.
Conformers are generated for the input molecule; thus, if the primary molecule has multiple conformers they are ignored.
This floe assumes that all input molecules are a part of the same ensemble. Since conformers are generated at the beginning, there is no reason to provide more than one input molecule. If multiple molecules are provided as input, they are all compared with the same global minimum and included in the same energy filter. Thus, it is generally recommended to only include one molecule unless multiple molecules are being considered in the same energy landscape, such as different tautomers or stereoisomers of the input molecule.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Input Dataset (in): The dataset(s) to read records from
Required
Type: data_source
Outputs
Intermediate Optimization Output (confgen_data_out): Dataset to store QM optimized conformers before deduplication. If a job is canceled early (either by the user or because a cost threshold is reached), these intermediate optimized conformers will still be saved.
Required
Type: dataset_out
Default: gau_all_conf_gopt
Gaussian Conformer Ensemble Output (gau_gopt_data_out): Dataset to store optimized conformers in the specified energy window. Each record has a single conformer.
Required
Type: dataset_out
Default: gau_confs_gopt_spe
Failure Output (failure): Dataset to store records which fail during this floe.
Required
Type: dataset_out
Default: gau_conf_ens_failures
Conformer Floe Report Name (conf_report_name): Floe report title that summarizes conformer ensemble results.
Type: string
Default: Gaussian Conformer Report
Backup Collection Name (collection_name): Name of collection to store backup checkpoint files.
Type: collection_sink
Default: Gaussian Backup Collection
Conformer Parameters
Constrain Torsions (constrain_switch): When turned On, torsions around all rotatable bonds are constrained during the geometry optimizations. Choose this option to get a diverse set of conformers spanning a wide range of energies. When the switch is turned Off, full geometry optimizations are performed without any constraints. Choose this option to get a sampling of low energy conformers.
Required
Type: boolean
Default: True
Choices: [True, False]
RMSD Threshold for Conformer Generation (confgen_rmsd_threshold): RMSD threshold for conformer duplicate removal
Type: decimal
Default: 0.5
Maximum Conformers (omega_max_confs): Set the maximum conformers to be generated with Omega. Note the more conformers the more expensive the QM optimizations will be.
Type: integer
Default: 100
Omega Energy Window (conf_en_window): Energy window used for conformer generation in Omega
Type: decimal
Default: 50.0
Gaussian Calculation Parameters
Gaussian Optimization Method (gopt_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 Optimization Basis Set (gopt_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’, ‘’]
Gaussian Optimization Solvent Environment (gopt_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 SPE Method (prop_method): Method used for this Gaussian calculation
Type: string
Default: B3LYP - GD3BJ
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 SPE Basis Set (prop_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’, ‘’]
Gaussian SPE Solvent Environment (prop_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 Energy Window (kcal/mol) (gau_energy_window): Energy window for filtering high strain conformers. Energy is calculated using all conformers from all input molecules. When the filter is set to -1, all conformers are included in output.
Type: decimal
Default: 10.0
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 Conformer Generation Options
Switch (csp_conf_switch): Use the extra dense conformer generation developed for OpenEye’s
crystal structure prediction protocol. In this algorithm, all fragment enumeration is maintained during deduplication.
Required
Type: boolean
Default: False
Choices: [True, False]
Maximum Conformers for Geometry Optimization (limit_confs): This parameter limits the number of conformers optimized to prevent accidentally spending more than expected on a single floe. If more than this number of conformers are generated, then only one conformer will be optimized to learn about the cost of this floe/conformer. If the maximum number of conformers is set to 0, then ALL generated conformers are optimized.
Type: integer
Default: 100
Advanced Parameters
Gaussian Optimization Energy Field (gau_opt_energy): Field created during Floes to store Gaussian Energy
Type: field_parameter::float
Default: Gaussian Opt. Energy (kcal/mol)
Gaussian Single Point Energy Field (prop_energy): Field created during floes to store Gaussian energy.
Type: field_parameter::float
Default: Gaussian Energy (kcal/mol)
Gaussian Strain Energy Field (gau_strain_energy): Field to store relative Gaussian energy between conformers.
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 (qm_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
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