SZYBKI - Single point MMPBSA

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 - Single Point MMPBSA calculates the MMPBSA score of a small molecule within a protein active site. A single point calculation is performed, and thus both the protein and ligand structures are kept intact during the calculation.

The minimal input into SZYBKI - Single Point MMPBSA is a design unit or a 3D protein structure, and a dataset of molecules in 3D format.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input DU/Ligand (in): Dataset containing design units or ligands. For ligand inputs, a second dataset of a Design unit must also be provided.

  • Required

  • Type: data_source

Input Design Unit (init): (Optional) Dataset containing design unit for docked ligands. An entry in this field assumes that ligands from the other dataset to be used for calculation against protein from this DU.

  • Type: data_source

Outputs

Output Dataset (out): Output dataset of successful calculations

  • Required

  • Type: dataset_out

  • Default: Output for SZYBKI - Single point MMPBSA

Failed Dataset (failed): Output dataset of failed calculations.

  • Required

  • Type: dataset_out

  • Default: Failed Output for SZYBKI - Single point MMPBSA

Forcefield and Charges

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

  • Type: string

  • Default: ff14sb_sage

  • Choices: [‘ff14sb_sage’, ‘ff14sb_parsley’, ‘mmff94’, ‘mmff94s’, ‘mmff_amber’, ‘mmffs_amber’]

Custom FF File (ff): Custom smirnoff force field file. Entry in this field creates a OEFF14SBSmirnoff force field and overrides any other force field selections

  • Type: file_in

Use input charges (inp_charges): Specify if input charges should be used if available. This flag is ignored if input ligand does not contain charges.

  • Type: boolean

  • Default: True

  • Choices: [True, False]