Computational Chemistry for Experimental Chemists

Jaguar (QM) Maestro

Other Apps

MacroModel (MM)

Opening Maestro
1. Mac: Open the Terminal (Finder Applications Utilities Terminal) Windows: Open X Win Server (Start Programs Cygwin-X X Win Server) 2. Type ssh -X username@vickyp.chem.columbia.edu Enter your password when prompted. 3. Type ssh -X surmgt1 Enter your password when prompted 4. Type ssh -X aqfctl Enter your password when prompted 5. Go to whichever directory you'd like to work in. For example, if I want to work in directory directory_name, I would change to that directory by typing cd directory_name You can think of cd as change directory. 6. Open up the Maestro GUI (graphical user interface) by typing $SCHRODINGER/maestro

Setting up a Job
1. Build the structure you desire in the Maestro window. Now we need to take what you've drawn and make it into something more physically reasonable using Molecular Mechanics (MM). 2. Go to Applications MacroModel Minimization. Run a minimization. This should take no longer than a few minutes to complete. (MM is fast.) When completed, import the results. 3. Now we will perform an MM conformational search to find the lowest energy conformation(s) of your structure. Applications MacroModel Conformational Search. This again should only take a few minutes, although it will take longer than the minimization. Import the results

when the job has finished. 4. You now have a Molecular-Mechanics refined structure. However, this is still pretty coarse. We will now minimize/optimize the structure with Quantum Mechanics (QM), a much more accurate method. Applications Jaguar Optimization 5. Once you have setup your optimization, DO NOT hit the Start button. Press the Write button adjacent to it. Save the file to the desired directory. We will start the job from the command line.

Running a Jaguar Job

1. Make sure you're currently in the directory where you're *.in file is located. This directory should also contain the script titled sge_serial_script 2. type emacs sge_serial_script A text editor will appear. Edit the job name and input file name to desired value Save and quit.

3. Type qsub sge_serial_script Your job is now running! 4. To check on the status of your jobs type qstat at any time. 5. Once completed, you may import the results into Maestro for viewing. In the above example, the results would be importable from the test.01.in and/or the test.01.mae files. Other useful information is contained in the test.log and test.out files, too.