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Glide Ligand Docking

Glide ligand docking jobs require a set of previously calculated receptor grids and one or more ligand structures. Preparation of the ligands before docking is strongly recommended. LigPrep or MacroModel can be used to prepare ligands. If a correct Lewis structure cannot be generated for a ligand, it will be skipped by the docking job.

Backend implementation

$SCHRODINGER/glide

Options

Column containing receptor input

Select the column containing Glide grid

Column containing ligands to be docked

Select the column containing the ligands to be docked

Output Column Structure

Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Settings...

On clicking "Settings" button, this node brings up the "Glide Ligand Docking" Python panel for configuration.

Read Maestro Settings...

On clicking "Read Maestro Settings" button, this node brings up a file browser. Browse to a 'Glide Ligand Docking' job diretcory written by Maestro and select the jobname.in file. The "Glide Ligand Docking" Python panel will now be opened by loading the settings read from the selected jobfile.

Parameter flow variables

Flow variable prefix keyword: GlideDockingInput
Use this prefix to control the Glide docking keywords in the input file (.in)
For example,
Flow variable name: GlideDockingInput-PRECISION
Flow variable value: XP

Flow variable prefix keyword: GlideDocking
Any valid command line option for this node can be specified through flow variables. Only String variables are accepted.
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option without a value, specify the option_name and the value as _off_ through the flow variable.

To remove an existing option with a value, specify the option_name and the value as _rm_ through the flow variable.

Input Ports

: Glide Grid
: Ligands in Maestro, Sd or Mol2 format

Output Ports

: Pose Viewer in Maestro or Sd format (i.e Receptor and docked ligands or only ligands)

Popular Predecessors

Popular Successors

Views

Log file: Log output
Subjobs log file: Subjobs log output

Workflows

Developers

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Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 24.3.138.v202407300410

On NodePit since: 2023-12-06

Last update: 2024-11-20

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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