A1. Protein Sampling (for Cryptic Pockets): Solvate and Equilibrate Target Protein

Category Paths

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

  • Product-based/Molecular Dynamics

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation/Enhanced Sampling

  • Solution-based/Target Identification/Target Preparation/Pocket Detection

  • Solution-based/Hit to Lead/Target Preparation/Cryptic Pocket Detection

  • Role-based/Computational Chemist

  • Task-based/Target Prep & Analysis/Pocket Detection


This floe can create a mixed (water-xenon) solvent or a single-solvent (water) box around a target protein and runs several stages of MD to equilibrate the system.

Promoted Parameters

Title in user interface (promoted name)


MD Output Collection Name (collection_output_name): Name of the MD output collection.

  • Type: string

  • Default: Solvated and Equilibrated MD Collection

Output Dataset (data_out): Output dataset to write to.

  • Type: dataset_out

  • Default: Solvated and Equilibrated Design Unit

Force Field

Protein Parameters (protein_forcefield): Force field parameters for the protein.

  • Type: string

  • Default: Amber14SB

  • Choices: [‘Amber14SB’, ‘Amber99SB’, ‘Amber99SBildn’, ‘AmberFB15’]

Ligand Parameters (ligand_forcefield): Force field parameters for the ligand (if present).

  • Type: string

  • Default: OpenFF_2.0.0

  • Choices: [‘Gaff_1.81’, ‘Gaff_2.11’, ‘OpenFF_1.1.1’, ‘OpenFF_1.2.1’, ‘OpenFF_1.3.1’, ‘OpenFF_2.0.0’, ‘Smirnoff99Frosst’]

Solvent Options

Padding Distance (padding_distance): The padding distance between the solute and the box edge (in Å).

  • Type: decimal

  • Default: 10

Salt Concentration (salt_concentration): The salt concentration (in millimolar). This does not include the ions required to neutralize the system.

  • Type: decimal

  • Default: 0

Solvents (solvents): Select solvents. This selection currently support Xenon and tip3p. To perform a single solvent simulation, specify only tip3p as the solvent here and change the “Solvent Molar Fractions” to 1.0.

  • Type: string

  • Default: tip3p, [Xe]

Solvent Molar Fractions (molar_fractions): Molar fractions for each solvent component. The molar fractions are specified as comma separated molar fractions strings e.g. 0.5, 0.2, 0.3. The default value (0.997, 0.003) is used to set the concentration of Xenon at 150 mM.

  • Type: string

  • Default: 0.997, 0.003