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XedMin

Cresset KNIME Nodes version 2.6.0.41359 by www.cresset-group.com

XedMin is a simple minimiser. It takes the input structures in SDF format, minimises each of them using the XED3 force field.

This node wraps the XedMin executable 'XedMin', which must be installed with a valid license for this node to work. If this is installed in the default location on Windows, then it should be found automatically. Otherwise, you must either set the 'Cresset Home' preference setting or the CRESSET_HOME environment variable to the base Cresset software install directory. You may also set the "xedmin" preference setting or the CRESSET_XEDMIN_EXE environment variable to point directly at the executable itself.

For more information visit www.cresset-group.com or contact us at support@cresset-group.com.

Options

Basic

Column containing molecule structure: The column in the input datatable containing the molecules to be minimised. These must be in SDF format.
Column containing (optional) protein structure: The column in the second input datatable which contains the optional protein structure, to be used to constrain the minimisation.

Advanced

Disable electrostatics and attractive vdW: This parameter controls whether electrostatics and attractive vdW forces are used in the minimisation. If checked, a pseudo-aqueous environment is simulated, at the expense of disregarding intramolecular hydrogen bonds etc
Max iterations: The maximum number of conjugate-gradient iterations to perform. Set to 0 for infinite iterations.
Gradient threshold on minimiser: RMS threshold (in kcal/mol/A) for considering the minimisation to have converged. Values of 0.5 down to 0.001 are sensible.

Input Ports

: Molecules to be minimised using the XED force field.
: Optional: One or more protein structures to be included in the minimisation as 'fixed atoms' - they will be included for energy calculations but are not allowed to move. Note that protein(s) read here will not be included in XedMin's output.

Output Ports

: The molecules which have been minimised.

Best Friends (Incoming)

XedeX (56 %)
Java Snippet (11 %) Streamable
SDF Reader (11 %)
RDKit Generate Coords (11 %) Streamable
RDKit Optimize Geometry (11 %) Streamable

Best Friends (Outgoing)

Workflows

Minimise a set of molecules inside a protein using XedMin (Cresset)

Installation

To use this node in KNIME, install Cresset KNIME Nodes from the following update site:

KNIME 4.3

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Developers

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