SZYBKI - Small Molecule Minimization

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/SZYBKI

  • Solution-based/Small Molecule Lead-opt

  • Task-based/Ligand Posing & Analysis

  • Role-based/Computational Chemist


SZYBKI - Small Molecule Minimization optimizes free ligands in the gas phase or in solution. Szybki Free Ligand is not setup to optimize protein-like structures and rejects such molecules to the failure port.

The minimal input into Szybki Free Ligand is a dataset of molecules in 3D format.

Promoted Parameters

Title in user interface (promoted name)

SZYBKI settings

Force Field (force_field): Built-in force field model to be used.

  • Type: string

  • Default: sage_openff200

  • Choices: [‘mmff94s’, ‘smirnoff99frost’, ‘parsley_openff100’, ‘parsley_openff111’, ‘parsley_openff121’, ‘parsley_openff131’, ‘sage_openff200’]

Custom FF File (ff): Custom smirnoff force field file. Entry in this field overrides any other force field selections

  • Type: file_in

Solvent model (solvent_model): Solvent model to be used for ligand

  • Type: string

  • Default: Gas-phase

  • Choices: [‘Gas-phase’, ‘Sheffield’, ‘PB’, ‘SheffieldPB’]