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RRHO Entropy

This Node Is Deprecated — This node is kept for backwards-compatibility, but the usage in new workflows is no longer recommended. The documentation below might contain more information.

This node runs a MacroModel Rigid Rotor Harmonic Oscillator (RRHO) calculation to obtain the change in translational, rotational, vibrational, and total entropy of the ligand upon binding. It generates a table with the entropies ( T*dS_translational, T*dS_rotational, T*dS_vibrational and T*dS_total). Optionally, the input Maestro file can be included in the output table.

The conformational entropy is not computed, since that would require a thorough sampling of the energy landscape of the ligand both in the environment of the protein and in solution in order to obtain the partition function.

Note that this node takes a pose viewer file as input, i.e. a Maestro file that has the receptor as it first entry followed by the ligands.

Backend implementation

rrho_entropy.py
The script rrho_entropy.py is used to implement this node.

Options

Column containing structure: Select column in the data input table containing the structures
Include ligands in output: Include ligands in output
Force Field: Available force fields: MM2, MM3, AMBER, OPLS, AMBER94, MMFF94, MMFF94s, OPLS_2005 (default)
Radius: Receptor atoms within this distance of the ligand to be included in bound state calculation. Note that the receptor residues create the potential field around the ligand, but are not themselves used to compute the entropy (in MacroModel terms, they are frozen).
Maximum Number of Processors: Maximum number of processors to use

Input Ports

: PoseViewer (Receptor and Ligands) in Maestro format

Output Ports

: Translational, rotational, vibrational, and total entropies for each ligand in the input table

Popular Predecessors

Popular Successors

Views

Log output of RRHO Entropy: Log output of RRHO Entropy

Workflows

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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: 2024-12-18

Tags: Deprecated

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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