RRHO Entropy
Schrödinger extension for KNIME Workbench version 4.6.12.201907040533 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.pyThe 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
Output Ports
Views
- Log output of RRHO Entropy
- Log output of RRHO Entropy
Best Friends (Incoming)
- Glide Ensemble Docking (100 %)
Best Friends (Outgoing)
- Column Filter (100 %) Streamable
Workflows
Installation
To use this node in KNIME, install Schrödinger extension for KNIME Workbench from the following update site: