Redundant Conformer Elimination Panel

The Redundant Conformer Elimination panel is used to eliminate conformers that are identical after either a conformational search or the minimization of a set of conformers. The elimination is based upon energies and distances between atoms. The energies used may be from a previous MacroModel or Jaguar calculation.

To open this panel, click the Tasks button and browse to MacroModel → Redundant Conformer Elimination.

  • Using
  • Features
  • Additional Resources

Using the Redundant Conformer Elimination Panel

MacroModel panels allow you to choose structures from either the Workspace or the Project Table. In the center of the Redundant Conformer Elimination panel you can set up the atoms to be used in structural comparison and set other criteria for comparison or elimination of atoms. Once you have finished configuring the settings on the panel, you can click Run to run the job with the current job settings, or you can click the Settings button to open the Job Settings Dialog Box to make job settings and run the job.

Structural comparisons can be performed "in place", that is, with no translation or rotation of the structures. This option is useful if the molecules have been positioned with respect to some kind of external potential such as that of a receptor. The comparison can also eliminate or retain mirror images of each structure.

In addition to the comparison of the geometries of the conformers, you can choose to include the energy as a criterion for comparison. The energy is used to pre-screen the structures for equivalence. If the energies of two structures are within 1 kJ/mol, the structures could be equivalent, and the structural comparison is done to check whether they are indeed equivalent. This option provides a very rapid screening of structures for equivalence. You can use energies from Jaguar as well as from MacroModel for the comparison criterion.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see bmin Command Help or macromodel Command Help. For information on the command file keywords, see the MacroModel Command Reference Manual.

Redundant Conformer Elimination Panel Features

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Comparison atoms controls

Define the atoms that are equivalent in each structure. These are the atoms that are used for the comparison that determines which structures are conformers. You can define the comparison atoms using the following:

The atom pairs are listed in the text area. If you want to delete a pair, select the pair in the list and click Delete. To delete all pairs, click Delete All.

Eliminate redundant conformers using options and Cutoff text boxes

Select the distance measure for determining whether structures should be considered equivalent:

  • Maximum atom deviation—consider structures to be different if the maximum atom deviation for any pair of corresponding atoms exceeds the threshold given in the Cutoff text box.

  • RMSD—consider structures to be different if the RMS deviation for all compared atoms exceeds the threshold given in the Cutoff text box.

The default cutoff is 0.5 Å for both options.

Compare structures 'in place' (no superposition) option

Select this option to compare the structures in their given locations: the conformers are not superimposed (translated and rotated to obtain the closest alignment of atoms) during the comparison process. By default, the structures are superimposed. This option may be useful for Glide poses, for example, where the position of the ligands with respect to the receptor is important.

Retain mirror-image conformations option

By default, both a structure and its mirror image are considered when comparing with the other structures. If one of the two matches, the structure is eliminated. To ensure that both the structure and its mirror image are kept, select this option.

Source of energy option menu

Choose an energy to include it as a criterion for comparison of the structures or choose None to disable the energy comparison. Structures whose energy differs by more than 4.184 kJ/mol (1 kcal/mol) are considered inequivalent. This test is applied before the geometries are compared,and can considerably speed up the comparison. You can choose from the Jaguar energy or the energies for various force fields supplied with MacroModel. If the particular energy you selected is not available among the properties of the structure, the calculation stops.

Energy window for saving structures text box

Specify the threshold value for comparison of structures. Structures are kept only if their energy is less than this value above the current global minimum. Lowering this value results in fewer structures saved. The default is 21 kJ/mol (5 kcal/mol).

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Minimization - Job Settings Dialog Box, where you can make settings for running the job.

The Job Settings button opens the Redundant Conformer Elimination - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

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