Psi4 QM Fragmentation and Torsion Scanning¶
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/Psi4
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 rotatable torsion in each fragment. Then a QM optimization is performed with the torsion constrained while all other degrees of freedom are relaxed.
Lastly, 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:
the fragments as multiconformer molecules, where each
conformer represents one angle from the torsion scan; and - the input (parent) molecules with the torsion rules for conformer generation.
The parent output can be used as input for the Psi4 QM Conformer Ensemble
or Psi4 QM Local Minima Search floes, 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: psi4_torsion_rule_output
Fragment Output (frag_out): Dataset to store fragment records with torsion scans.
Required
Type: dataset_out
Default: psi4_fragment_output
Failure Output (failure): Dataset to store records which fail during this floe.
Required
Type: dataset_out
Default: psi4_fragmentation_failures
Fragmentation Report Title (frag_floe_report_name):
Type: string
Default: Psi4 Fragmentation Report
Torsion Parameters
Torsion Increment (resolution): Torsion increment angle in degrees for the scan.
Type: decimal
Default: 5.0
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]
Psi4 Calculation Parameters
Psi4 Hamiltonian (Torsion Scan) (torsion_method): Method used for geometry optimizations in torsion scans.
Type: string
Default: HF3c
Choices: [‘HF3c’, ‘PBEh3c’, ‘HF’, ‘HF-D3’, ‘B3LYP’, ‘B3LYP-D3BJ’, ‘B3LYP-D3MBJ’, ‘B2PLYP-D3BJ’, ‘M06’, ‘M06-2X’, ‘M06-L’, ‘MN15-D3BJ’, ‘MN15-L’, ‘PW6B95-D3BJ’, ‘CAM-B3LYP’, ‘CAM-B3LYP-D3BJ’, ‘WB97X’, ‘WB97X-D’, ‘WB97M-D3BJ’, ‘B97M-D3BJ’, ‘PBE’, ‘PBE0’]
Psi4 Basis Set (Torsion Scan) (torsion_basis): Basis set used for geometry optimizations in torsion scans.
Type: string
Default:
Choices: [‘’, ‘minix’, ‘6-31G’, ‘6-31G*’, ‘6-31+G*’, ‘6-31G**’, ‘6-31+G**’, ‘6-311G**’, ‘6-311+G**’, ‘6-311G(2d,2p)’, ‘def2-SVP’, ‘def2-SVPD’, ‘def2-TZVP’, ‘def2-TZVPD’, ‘def2-TZVPP’, ‘def2-TZVPPD’, ‘DZVP’, ‘cc-pVDZ’, ‘aug-cc-pVDZ’, ‘cc-pVTZ’, ‘aug-cc-pVTZ’, ‘LanL2DZ’]
Psi4 Memory (Torsion Scan) (torsion_memory): Memory for Psi4 calculations in MBs
Type: decimal
Default: 14400
Psi4 #Threads (Torsion Scan) (torsion_nthreads): Number of CPUs for Psi4 calculations.
Type: integer
Default: 8
Optimization Engine (psi4_engine): Chose an engine for the geometry optimization. Psi4
supports both OptKing and GeomeTRIC.
Type: string
Default: Psi4 GeomeTRIC
Choices: [‘Psi4 OptKing’, ‘Psi4 GeomeTRIC’]
Advanced Parameters
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
Psi4 Energy Field (frag_energy_field): New field created on torsion scan output to store QM energy at each torsion angle.
Required
Type: field_parameter::float
Default: Psi4 Energy (kcal/mol)
Psi4 Strain Energy Field (frag_strain_energy_field): 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: Psi4 Strain Energy (kcal/mol)
Save Psi4 Log File (store_log_file): The log file generated from Psi4 is saved. It will be available as a floe report when the floe is complete.
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: Psi4 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 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)