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   maestro/macromodel/jaguar frequently asked questions
Chemical Information Laboratory

Maestro/MacroModel/Jaguar FAQ

Where are my molecules?
The Project Table does not record molecules' structures - it simply keeps track of the different files which hold the structures. If you draw a structure on the screen, but do not do a calculation on it nor Export it to a file, it will be lost when you stop running Maestro. If you use MacroModel or Jaguar to do a calculation, it will create a series of files which include the molecular structure. If you do two different calculations with the same filename, the first calculation will be deleted by the second.

What is mmodtmp?
This is the default filename for MacroModel calculations. If you are doing a quick and simple calculation, it may be convenient to use it, rather than choosing a new filename, which could take several seconds. However, running such a calculation will delete any earlier calculation done with the same name, so the seconds saved increase the danger of overwriting your work with a new calculation.

How do I centre my molecule on the screen?
Click the Fit button, which it towards the lower right hand corner of the Maestro window.

Why doesn't my conformation search start?
Have you gone to the CSearch window and clicked Perform Automatic Setup?

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department of chemistry University of Cambridge