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MMFF94 Minimizer

LigandScout Extensions for the KNIME Workbench version 1.8.0 by InteLigand GmbH

The MMFF94 Minimizer node allows the energy minimization of molecules and/or side chains.

Options

Settings

Stopping criterion: Energy delta
If selected, the tolerance value specifies a difference in energy between two optimization iterations. If the calculated energy difference is lower than the specified delta, the optimization is stopped.
(Default: disabled)
Stopping criterion: RMS gradient
If selected, the tolerance value specifies the root mean square of the energy gradient components. If the calculated RMS gradient is lower than the specified value, the optimization is stopped.
(Default: enabled)
Tolerance
Defines the value of the RMS gradient or energy delta.
(Default: 0.25)
Max. number of iterations
Defines the maximum number of optimization iterations to perform. A value of -1 specifies that the optimization is performed until the rms gradient or energy delta is reached.
(Default: -1)
Minimize molecule
If unchecked, molecules are rigid
Minimize sidechains
If unchecked, sidechains are rigid

Active Site Settings

Select all active sites for which minimization should take place (Default: All active sites found).

Force Field Settings

General MMFF94 settings. Defaults should cover most use cases.

Input Ports

Icon
Table containing the macromolecule(s)

Output Ports

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Table containing the minimized macromolecule(s)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

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

KNIME 4.3

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Developers

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