QM Conformer & Tautomer Predictor Panel

Generate the lowest energy tautomers or conformers (or both) for a set of structures, with optional protonation or deprotonation.

To open this panel: click the Tasks button and browse to Quantum Mechanics → QM Conformer and Tautomer Predictor.

  • Overview
  • Using
  • Features
  • Additional Resources

Overview of QM Conformer and Tautomer Prediction

The prediction of the lowest energy conformer and tautomer is performed in several stages.

  1. The proton donor and acceptor atoms are identified, and protons are redistributed among these to form a list of tautomers. Protons can also be added to or subtracted from the input molecule.

  2. The tautomers generated are ranked by their semiempirical PM3 heat of formation, and the high-energy tautomers are discarded.

  3. Conformers are then generated for the surviving tautomers (with MacroModel).

  4. The resulting structures are then filtered again by their semiempirical PM3 heat of formation, to eliminate high-energy structures.

  5. DFT geometry optimizations are performed on the surviving structures, using the B3LYP-D3/LACVP** level of theory.

  6. The structures are ranked using single-point energies at the M06-2X/cc-pVTZ(-f) calculated at the optimal geometries from the previous step.

Using the QM Conformer & Tautomer Predictor Panel

The intended use of this panel is to ensure that the structures you use for some other calculation are performed on the lowest energy tautomer or conformer. Using the lowest energy structure is important for FEP+ calculations and for Jaguar pKa calculations, for example.

If you want to customize the workflow, you can do so by clicking the arrow next to the Settings button on the job toolbar, and choosing Use custom configs. The dialog box that opens allows you to change the stages and the settings for each stage, and then run a job with these settings. The settings made in this dialog box do not change the settings in the main panel; if you don't change anything in the main panel or run a job, the settings in the dialog box are preserved when you reopen it.

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 AutoConf.py Command Help. See also AutoConf.py: Generate Lowest-Energy Tautomers and Conformers.

QM Conformer & Tautomer Predictor Panel Features

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
  • Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

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.

Generate option menu

Choose whether to generate conformers, tautomers, or both. If generating both, tautomers are generated first, then conformers are generated for each tautomer.

Options link

Specify options for ring tautomerization, addition or removal of protons, and solvent. Opens the QM Conformer & Tautomer Predictor — Options Pane.

Keep options and text box

Select an option to specify the number of structures to keep. The time taken increases with the number of structures that are kept.

  • Top—select a number of structures to keep, specified in the text box. The structures are selected in order of increasing energy.
  • All—keep all the generated structures.
Job toolbar

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

The Job Settings button opens the QM Conformer & Tautomer Predictor - 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.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

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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