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 creates a solvent (water) box around a target protein with 150 mM NaCl and 150 mM Xenon (probe) and runs several stages of MD to equilibrate the system. Users have an option to change the solvent condition to single-solvent.

Promoted Parameters

Title in user interface (promoted name)

Input Data

Target Protein (data_in): A protein structure prepared by SPRUCE (preferred method). If more than one record is provided, only the first will be processed by this floe.

  • Required

  • Type: data_source

Output Data

Solvated and Equilibrated Protein (a1_data_out): Dataset to which to write the solvated and equilibrated protein.

  • Type: dataset_out

  • Default: Solvated and Equilibrated Protein

Failure Report (failure_report): Output report to generate upon failure.

  • Type: string

  • Default: Solvate and Equilibrate Failure Report

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

  • Type: string

  • Default: Solvated and Equilibrated MD Collection

Force Field

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

  • Required

  • Type: string

  • Default: Amber14SB

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

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

  • Required

  • 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’, ‘OpenFF_2.2.0’, ‘Smirnoff99Frosst’, ‘Custom’]

Solvent Options

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

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: 150