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