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RRHO Entropy

DeprecatedDeprecated Nodes version 21.1.156.202102141445 by Schrödinger

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

Views

Log output of RRHO Entropy: Log output of RRHO Entropy

Best Friends (Incoming)

~~Glide Ensemble Docking~~ (67 %) Deprecated
~~Glide Ligand Docking~~ (33 %) Deprecated

Best Friends (Outgoing)

Column Filter (50 %) Streamable
Lookup and Add Columns (50 %)

Installation

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

KNIME 4.3

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Developers

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