How to use Webmo to create and manage Gaussian quantum chemistry calculations

1. Connect to helen.chem.haverford.edu

1. Choose helen, priam, or hecuba and click on the link to the WebMO server for that computer. Superlab users should have accounts on all three of these servers.
2. Log in to your account at the WebMO prompt. This will take you to the job manager.
3. To create a new job:
   1. click on "new job: create new job" and do one of the following:
      1. Use the WebMO editor. In the "Build Molecule" window, click on "Open editor" and a new window will pop up. Create your molecule using the simple buttons on the left. WebMO will create a z-matrix for your molecule as you go along. Keep in mind: if there are colinear atoms in your molecule (i.e. a 180 bond angle), you should use pasted-in coordinates (see next option) rather than the builder.
      2. Enter a blank molecule and manually paste in the coordinates later. For complicated molecules (e.g. more than 20 atoms, and/or complicated 3-D structure), use this option. Do nothing in WebMO here; however, you should create a text file that contains either Cartesian coordinates or a z-matrix for the atomic positions and have this ready for pasting purposes. Note: do not use the import job command unless you have an existing Gaussian output file. It is very difficult to get WebMO to import text files and recognize them as valid inputs
   2. Once your molecule has been built (or skipped for later), close the editor (if needed) and click on the right arrow on the Build Molecule page.
   3. On the Configure Gaussian Job Options page, make sure that you inspect and change all input fields at the "Job Options" tab. Mistakes here will make your final job meaningless. Be sure to use a clear and evocative job description, and enter this description (and values for all input fields) in your lab notebook. Note that for the pull-down menus, Gaussian offers many more options than the WebMO menus; make sure that any text you enter manually conforms to Gaussian input per the online Gaussian input manual.
   4. When satisfied with Job Options values, click on the Preview tab.
4. A blank window will appear. Click "Generate" and this will show you the text input file to be sent to Gaussian for calculations.
   1. If you built your molecule using the editor, inspect the input file and click the right arrow to submit the job.
   2. If you are pasting in coordinates, paste all coordinate lines from your text file below the line that contains two integers (i.e. 0 1). Make sure of two things:
      1. There is a blank line between the title and the line with the two integers.
      2. There is no blank line between the two integers line and your coordinates.
      3. There is at least one blank line at the bottom of the file after your coordinates.
   3. If all of the three preceding conditions are satisfied, then click on the right arrow to submit the job. A warning will pop up: answer this in the affirmative.
5. Once the job has been submitted, you will return to the Job Manager with your job at the top of the list. Make sure that the job is running (click "refresh" to make sure that it is actually moving forward). Look at the output file to make sure that everything is as expected.

Important web resources:
Webmo users manual: large .pdf file
Gaussian online input manual