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   macromodel
Chemical Information Laboratory

MacroModel


MacroModel is most conveniently used with the Maestro interface.
  • Documentation as PDF files in the directory: /usr/glea/schrodinger/docs/mm8/pdf/

  • Long calculations, such as conformation searches and molecular dynamics should always be run by submitting to the batch queue. When the calculation has been set up, do not click Start but click on Write Job Files instead. This creates files called filename.mae and filename.com. Type bminbat filename on the command line to send the job to the batch queue.

  • Helpful commands
    • bminbat filename: Submits calculations to the batch queue
    • mmck filename: Checks the progress of a conformation search

Once a molecule has been imported to or built in Maestro, MacroModel will do force-field energy calculations on it. The simplest of these is a single point calculation

Current Energy: (Menu: MacroModel->Current Energy...)
This will calculate the energy of the molecule, exactly as it is drawn. Selecting this option from the menu will create a new panel, allowing you to select a filename for the calculation (default: mmodtmp), a force field (default MM2*) and to start the calculation. A new window will appear (Monitori), giving the results of the calculation, including any errors if the force field does not recognise all of the molecule. The results of the calculation are also written to files:
mmodtmp.com mmodtmp.log mmodtmp.mae mmodtmp-mon.mae mmodtmp-out.mae
This will overwrite any earlier versions of the files, so it is important to choose good filenames. This replaces 'ECalc' from earlier versions of MacroModel.

Minimisations: (Menu: MacroModel->Minimization...)
A molecule that has been built in Maestro will generally not have a perfect geometry, and so the result of a single point calculation is likely to be a big number which relates to the precise molecular geometry which has been given to MacroModel. It would be much more useful to be able to draw an approximate geometry and have MacroModel turn it into a better geometry. Minimisation is the process of making small changes to the geometry so that the energy goes down, and stops when all small changes result in an increase in energy.

Choosing this option (Menu: MacroModel->Minimization...) gives a similar panel to that seen for single point calculations, but with rather more options. Pressing the start button will again generate the Monitori panel, which will follow the calculation. The geometry of the structure in the workspace will change as the calculation progresses. The energy that results from minimisation is usually more useful than that from a single point calculation, as anybody who sketches a simple molecule, for example, ethane, and minimises it with the same choice of force field and other parameters, should always get the same answer.

Conformation search: (Menu: MacroModel->Conformational Search...)
Minimisations do not always give the results you might expect, however. If two people draw cyclohexane and minimise it, one might get a chair conformation and the other a twist boat. These have different energies. For most molecules it is necessary not only to minimise a geometry but also to explore the conformation space of the system, to ensure that all minima have been found. The conformation search option does this.




© Goodman Group, 2005-2017; privacy; last updated October 18, 2017

department of chemistry University of Cambridge