XedeX

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

Specify how the conformation hunter is to handle amides.

• Force amides trans - forces all secondary amides to adopt the trans geometry.
• Use input amide geometry - leaves secondary amides in the geometry that they were in the input file and sets them as non-rotatable. As a result, if the input molecule was drawn with a cis amide then only conformations with cis amides will be generated.
• Allow amides to spin - allows the amide bond to spin, so a mixture of cis and trans amides can be generated.

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 generally decreases the quality 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.

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Workflows

• Generate conformations for a set of molecules using XedeXCresset

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