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XedeX

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

XedeX is a program to read in one or more molecules in and perform a conformational hunt using the XED force field. The conformational hunt process is designed to generate a highly diverse set of conformations, all of which are minimised, in the shortest time possible.

This node wraps the XedeX executable 'XedeX', 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 "xedex" preference setting or the CRESSET_XEDEX_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 containing the structures that should be processed by XedeX.
Number of conformations to keep
The maximum number of conformations to keep per molecule.

Advanced

Disable electrostatics and attractive vdW
This parameter controls whether electrostatics and attractive vdW forces are used in the conformer generation. If checked, the conformers present a better sampling of conformation space for an aqueous environment, at the expense of disregarding intramolecular hydrogen bonds.
Handle secondary amides
By default, amides are fixed in the input conformation. If 'Spin' is specified then amidic bonds are spun, while if 'Force trans' is specified then acyclic secondary amides are forced to the trans conformation.
Use a ring library with flexible rings
XedeX stores a library of flexible ring conformations. If this box is checked, any matching rings in a molecule will have their conformations populated from the library. If unchecked, or not all the molecule's rings are present in the library, dynamics runs as specified in the 'Number of dynamics runs if flexible rings present' option are carried out.
Number of dynamics runs if flexible rings are present
Specifies how many dynamics runs are performed for molecules for flexible rings. Specify 0 to turn off dynamics.
Energy window for output conformations
Energy window (in kcal/mol) in which to collect conformations. Conformations which are more than this value higher in energy than the lowest energy conformation found are discarded.
Conformation filter RMS
If two conformations have an RMS difference over all heavy atoms of less than this value (in A) then they are considered to be the same and only one is output.
Minimizer bailout RMS
RMS bailout on the energy minimisation (in kcal/mol/A). The default value gives a fast and loose minimisation, but no really bad interactions should be present. Minimising to a very low RMS value geneally decreases the qulity of the conformation search.
Don't write enantiomeric conformations for achiral molecules
By default enantiomeric pairs of conformations are both written. This provides a speed increase if the output is to be used in a Forge Align node, but may not be what is desired if the conformers are to be used in other analyses.

Input Ports

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A table containing at least one SDF molecule.

Output Ports

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A table containing the generated conformations in SDF format.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

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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