Ethylene is a simple organic molecule, of formula C₂H₄. The structure is shown below.

A data-set for the optimization of ethylene could be:

   Line   1  :  AM1 T=600 NOINTER VECTORS LOCAL EF
   Line   2  :  EXAMPLE OF MOPAC DATA-SET FOR ETHYLENE
   Line   3  :  The only geometric constraint is that the system must be planar
   Line   4  :  C  0   0    0 0    0  0  0 0 0
   Line   5  :  C  1.3 1    0 0    0  0  1 0 0
   Line   6  :  H  1.1 1  120 1    0  0  2 1 0
   Line   7  :  H  1.1 1  120 1    0  0  1 2 3
   Line   8  :  H  1.1 1  120 1  180  0  1 2 3
   Line   9  :  H  1.1 1  120 1    0  0  2 1 5
   Line  10  :

The first line consists of keywords (here six keywords are shown). These control the calculation. It is common to start with the choice of the method (MNDO, MINDO3, AM1, PM3) and a time statement (T=600) in seconds. This value corresponds to the time available in our fast queue, 10 minutes. For larger jobs the medium queue, time limit 3600 seconds, or even the long queue (21600 seconds) should be selected from the MOPAC submit menu.

The next two lines are comments or titles. The user might want to put the name of the molecule and why it is being run on these two lines.
Lines one through three are obligatory. If no name or comment is wanted, leave blank lines. If no keywords are specified, leave a blank line. Whatever is decided, the three lines, blank or otherwise, are obligatory.

The next set of lines defines the geometry.
The geometry data, starting on line 4, should be read as:
atom-symbol distance flag angle flag dihedral flag ref-atom-dist ref-atom-angle ref-atom-dih.
For this calculation, the starting values for bond-lengths and angles can be approximated. Whether or not MOPAC will optimize a variable is determined by the flag following it. A "0" turns the previous number into a constant, a "1" initiates optimization (which means in general: minimization of the energy).
For this system, the bond lengths and angles will be optimized. The torsion angles (zero and 180 degrees) are followed by a "0", because we know beforehand that the molecule is flat.

The last three numbers on each line define the previous variables.
E.g.: line 7 contains the data for the fourth atom, a hydrogen. The length is to atom 1, the angle is H4-C1-C2, and the dihedral angle is H4-C1-C2-H3.

Line 10 is a blank line and terminates the geometry and (in this example) the data-file. Any additional data, such as symmetry data, would follow line 10.

In the example, the numbers are all neatly lined up; this is not necessary, but does make it easier when looking for errors in the data.

This file should be saved as a .dat file, e.g. ethylene.dat. When MOPAC is selected from the menu, this name should appear in a selector box. Use the arrow keys to select the proper file and a queue, then activate the 'Execute' button. The job will run in the background. Upon completion a number of files ethylene.* will be produced, from which the .arc and .out file contain the result.
See MOLDEN or SYBYL on how to display the result.

Last updated on August 13th 1996