Semiempirical Module Panel

In this panel, you can set up and run a semiempirical calculation on one or more structures using the MOPAC code.

To open this panel, click the Tasks button and browse to Quantum Mechanics → Semiempirical.

For information on running from the command line, see Running a Semiempirical Module Job from the Command Line.

  • Features
  • Additional Resources

Semiempirical Module Panel Features

 

Use structures from option menu

Choose the structure source for the semiempirical calculations.

  • 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—Use the contents of the Workspace as a single structure.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed. The allowed file types are: Maestro, SD, or MOL2.
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.

Method option menu

Choose the method to use from this option menu. The available methods are AM1, RM1, MNDO, MNDO/d, and several PMn methods: PM6, PM6-D3, PM6-DH+, PM6-DH2, PM6-DH2X, PM7, and PM7-TS [3, 4]. The variants of PM6 are corrected for one or more of dispersion, hydrogen bonding, and halogen bonding. PM7-TS is intended only for barrier heights of transition states.

Charge text box

Specify the charge on the molecule in this text box.

Multiplicity text box

Specify the spin multiplicity of the molecule in this text box. The maximum allowed multiplicity is 6.

Wavefunction option menu

Specify the spin treatment of the wave function. When the multiplicity is not 1, you can choose between ROHF (the default) and UHF.

Molecular and atomic properties section

Select options for the calculation of atomic and molecular properties. With the exception of bond orders, the properties are added to the Maestro output file as atom or entry properties. The options are:

  • Mulliken charges—Calculate atomic charges from Mulliken population analysis (MULLIK keyword).
  • Bond orders—Calculate bond orders, including sigma-pi components (BONDS and PI keywords).
  • SAR properties—Calculate HOMO and LUMO energies, molecular hardness and electronegativity, electrophilic and nucleophilic frontier electron densities (electrophilic, nucleophilic, and radical superdelocalizabilities, and atom self-polarizabilities SUPER keywords).
Plot properties section

In this section you can select the properties to tabulate on a grid for display in Maestro as surfaces. Currently, only molecular orbital plotting is available. You can choose how many orbitals on either side of the HOMO-LUMO gap are plotted. In addition, you can set the grid resolution (points per Å) and the grid extension (beyond the van der Waals radii of the atoms, in Å) for the plots.

Optimize geometry option

Select this option to optimize the geometries of the input molecules; deselect it to run single-point calculations. The default is to optimize geometries.

If you are running a calculation on a large structure (1000 or more atoms), you can add the MOZYME keyword to speed up the calculations, especially if you are running on biological systems, for which this keyword was designed.

Archive output files option

Archive all the .out files to a zip file, which is named jobname.zip and is copied to the launch directory. If this option is deselected, the .out files are copied back individually to the launch directory, one for each structure. The default is to archive the .out files.

Keywords text box

Enter any additional keywords in this text box. See the Semiempirical Module Guide — Contents for more information on supported keywords.

Job toolbar

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

All structures are run in a single, serial job, and the results are returned in a single Maestro file. The calculations for each structure are very fast; however, if you want to distribute a job you can do so from the command line—see Running a Semiempirical Module Job from the Command Line.

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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