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Glide Grid Generation

Generates a Glide Grid from receptors or complexes. The node takes in 3 basic arguments, two of them (Center and Size) that can be specified either manually or by a Ligand. If a Ligand is needed in either of these arguments (Choose "Center of ligand" under Center, or "Ligand" under Size), then the Ligand needs to be specified (using the "Specify Ligand by" ComboBox). The third argument HBond Constraints can be specified by a string.

Backend implementation

utilities/generate_glide_grids
generate_glide_grids under utilities is used to implement this node.

Options

Save Grid: Whether the workflow saves the grid data (otherwise it saves a pointer to the files that exist on the file system)
Center of ligand: The center of the ligand is used as the Center of the grid generation
Supplied X,Y,Z coordinates: Specify X,Y, and Z as the Center of the grid generation
Size Ligand: The size of the ligand is used as the Size of the grid generation
Size supplied values: Supply the Inner and Outer Box values to be used in the grid generation
Specify Ligand by: Options are Default ASL, Specified ASL, or the ASL in a column
HBond Constraints: Input a string of colon-separated H-bond constraints, specifying a user-defined label, which must be unique, followed by '#' and the atom number for any metal atom, polar H, N, or O atom in the receptor. Glide will automatically include symmetry-equivalent atoms. Example:'label1#atomnum1:label2#atomnum2:label3#atomnum3'
Parameter flow variables: Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: GridGen
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 from command line, just specify the option_name and the value as _off_ through the flow variable.

Input Ports

: Receptor or complex(es) in Maestro Format

Output Ports

: Glide Grid

Popular Predecessors

Popular Successors

Views

Log file: Log file

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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