Modelling Instructions: GAMESS

Instructions for Use of the MacMolPlt and GAMESS Programs

These instructions contain the mimimum to get you going. A more complete set is available here. GAMESS is available on all Mac computers (i.e. not just the ones with CAChe on them).

GAMESS has a fairly primitive structure editor of its own, and the best way to define a molecule is to build it using another program, save the coordinates in either PDB (Brookhaven) or MDL (Molfile) format, and read that within the GAMESS program. The procedure using the CAChe editor is suggested here, although other programs (e.g Chem3D) could also be used to create a PDB or Molfile. Having drawn a molecule using the CAChe editor, and save the CAChe file in either format. This procedure is also useful since it illustrates how data can be passed from one program to another.
Next, open the program called MacMolPlt and in the File/Open dialog, select the PDB/Molfile file you have just created. A Window should open, and you can check that the integrity of your molecule is still intact.
You will now need to define the parameters for the GAMESS calculation. The default settings unfortunately are not entirely appropriate. Open the Input builder option;
In the basis group, the atomic orbital basis set must be selected. STO-3G will result in a reasonably quick calculation (and could be used to test that the calculation is properly set up); 4-31G provides a reasonably accurate wavefunction; 6-311G a much better one, but may take several days! Do note that as the accuracy of the basis set increases, so does the calculation time (more or less as the fourth power of the total number of basis functions!).
From the control group, select the Run Type as optimisation.
From the System required control group, select Megabytes from the Memory pull down menu, and set the value to about 60.0 (some G3 Macs have 128 Mbytes of memory fitted, in which case on those systems, you can set the memory up to about 80.0 Mbytes. The more memory you select, the more efficient will the calculation be.
From the SCF optional control group, check the Direct SCF button. This will evaluate all the integrals in memory rather than using the hard disk to store intermediate results. The more memory you can allocate in the step above, the better will this process be.
As the final step, click on the Write file button, and give your file a name such as alkene.inp.
If for some reason, you want to go back to re-edit the settings, you can do do either by double clicking the .inp file, or instead opening it with a standard text editor such as BBEdit. Some more interesting options in GAMESS are indeed only selectable with such a text editor. Two you might investigate are the Density Functional option and the COSMO solvation option. To invoke either, add one (or both) of the following lines to the control cards in the .inp file using an editor.
```
 $DFT DFTTYP=B3LYP $END
 $COSGMS EPSI=80.0 $END
```
BUGFIX The file just created (ending in .inp) is a text file with so-called Unix end-of-line characters. This will not run for the next program unless its end-of-line characters are changed to Macintosh. Do so using the BBedit editor (double clicking the file should open it in this editor).
Now find the program GQueue in the Applications/MacGAMESS folder and "drag-n-drop" your alkene.inp file onto this program.

A "batch queue" will be set up, and the MacGAMESS program proper will start running. You can add further jobs to the queue if you wish to stack them up.

Depending on the size of the molecule, and the size of the basis set chosen, the run may take anything between 40 min (6-31G on molecule 13) to 30 hours (or even more!). During this period, various scratch disk files will be created, which may occupy up to 2 Gbyte or more of disk space. You should periodically check that the hard disk has not filled up! The eventual result of the calculation will be written to a file called e.g. alkene.LOG. This text file contains all the information from the calculation, but you will probably not wish to use it as such. Whilst the GAMESS program is running, you can use the computer for other tasks, but you may find the response is not as fast as normal.
It is best at this stage to open the .LOG file using the MacMolPlt program by drag-n-dropping it onto the MacMolPlt dock item;

To get the best display, select QuickDraw 3D.
The calculated energy (in Hartree, or atomic units. 1 Hartree = 627.5 kcal/mol). of the molecule will be displayed in the bottom left information bar. The slider bar to the right of the energy will show you the energies as a function of each step in the geometry optimisation. If you move the slider to the right, you can then "export" the last, and presumably optimised, geometry of the molecule, again as a MDL Molfile which can be read into other programs.
To inspect the molecular orbitals and their energies, open the surface panel;
Select the type of surface to calculate by first clicking on "add";
Select an orbital to display. The orbitals are listed with the most stable at the top, along with the orbital energies (expressed in Hartree, or atomic units; to convert to e.g. electron volts, multiply these values by 27). Note that all bonding orbitals (occupation number 2 or 1) have negative energies; all unoccupied orbitals have +ve energies.
From the edit/copy menu of MacMolPlt the orbital picture can be copied to the clipboard, and pasted into e.g. a Word processor etc. Make a note of any orbital energies.
Coordinates can be exported from MacMolPlt using the File/Export menu item and selecting XMol-xyz type. These coordinates can be used directly within e.g. a Web page or as further input for a GAMESS calculation.
The above screenshots indicate numerous other options are available within the MacMolPlt and GAMESS program. You are encouraged to experiment with them!
You can also use GAMESS to prepare an input for other programs, such as e.g. Gaussian. Proceed as follows;
1. In the Input builder option of MacMolPlot, go to the Misc. Prog. Optional Control group, and check the Gaussian 9.X box.
2. Save the file, having selected other options such as Basis set etc.
3. Run GAMESS by drag-n-dropping the GAMESS input file onto GQueue
4. This will create a file ending in .DAT. Open this file in a text editor (e.g., BBEdit). You will see an entry beginning:
  -------- START OF -GAUS- INPUT FILE ----------
  Following the instructions here, and create a new file with the resulting contents. This can be used to run a Gaussian Job.

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