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
Description
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)
Outputs
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