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

Description

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

• Choices: [‘mmff94s’, ‘parsley’, ‘sage’]

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’]