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Glide Grid Generation

Schrödinger extension for KNIME Workbench version 20.3.139.202008120556 by Schrödinger

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)
Include Log in Output
The log is included in the output as a column
Include Out in Output
The out file is included in the output as a column
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

Icon
Receptor or complex(es) in Maestro Format

Output Ports

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Glide Grid

Views

Std error of generate_glide_grids
Std error of generate_glide_grids

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

KNIME 4.2
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Developers

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