Parametrizer GUI

Parametrizer WaNo

Input files and parameters: (Parametrizer tab)

Molecule Settings:

• Molecule (Mol2): Input of a 3D molecular structure in the mol2-file format.
• Molecule Identifyer: three-digit alphanumeric string that is used to label the molecule throughout the workflow in various output files.
• Optimize Molecule: Check this box to perform geometry optimization of your compound.

DFT Engine:

• Engine: Chose the DFT Engine for geometry optimization and computation of partial charges. Currently available: Turbomole (DFT, user needs to have a Turbomole license), Psi4 (DFT) and DFTB+ (DFTB). For details, check the DFTEngines-section
• Engine-specific settings:
  • Turbomole:
    • Partial Charge Method: Electrostatic potential fit (EPS) or Mulliken available. ESP recommended.
    • D3 Dispersion Correction: Account for Pauli-repulsion. We recommend to use this option for geometry optimization.
    • Functional and basis set: Check the Turbomole manual for details. We recommend to use B3LYP, SV(P) and the ESP-fit method for computation of partial charges.
    • DFTB3 Preoptimization: Preoptimization of the molecular geometry with DFTB may achieve a significant reduction of computation time. We recommend to use this option for molecules containing only elements supported by DFTB (see list of supported atom types )
    • SCF and Geometry convergence sets the Turbomole convergence criterion. For the subsequent computation of sensitive quantities such as excitation energies in QuantumPatch, we recommend to use the Tight or Extreme option, but stick to Normal otherwise.
  • Psi4:
    • Partial Charge Method: Electrostatic potential fit (EPS) or Mulliken available. ESP recommended.
    • D3 Dispersion Correction: Account for Pauli-repulsion. We recommend to use this option for geometry optimization.
    • Functional and basis set: Check the Psi4 manual for details.
    • DFTB3 Preoptimization: Preoptimization of the molecular geometry with DFTB may achieve a significant reduction of computation time. We recommend to use this option for molecules containing only elements supported by DFTB (see list of supported atom types )
  • DFTB+:
    • Partial Charge Method: Improved Charge Model 3 (CM3) or Mulliken available. CM3 recommended.
    • D3 Dispersion Correction: Account for Pauli-repulsion. We recommend to use this option for geometry optimization.

Parallelization and Performance: (Resources tab)

For every option not checked in the „Resources“ tab, the server defaults that depend on your HPC machine will be used. Check individual options to modify specific values.

Recommended resources for Parametrizer:

Resource	Recommendation
CPUs per Node:	The Parametrizer is parallelized up to a single node. We recommend to use a full node especially for larger compounds, if Turbomole or Psi4 is used.
Number of Nodes:	1
Memory:	1500MB
Walltime:	Computation time depends strongly on DFTEngine, size of the compound and number of cores, whether or not the geometry is optimized and if so, also on the quality of the initial geometry provided as input.
Queue:	Default

Output Files

Filename	File description	Interface to module...
molecule.pdb	pdb-file containing atom positions and bond information.	Deposit or DihedralParametrizer
molecule.spf	Force-field file for Deposit including partial charges and Lennard-Jones parameters as well as information on dihedral angles for the DihedralParametrizer.	Deposit or DihedralParametrizer