In protein work, all the systems you will be working with are very large, typically several thousand atoms. It's easy to get lost in such large systems, and if you don't know, or are not comfortable with, how MOPAC works, it would be doubly difficult. So before starting any work, run several small (four to ten atom) systems, to get a feel for what is involved.
But before doing anything, a few definitions are needed. In the instructions, some terms, such as "data set", "job", "calculation", and "step" are often used. In MOPAC work, these terms have the following meaning:
A data set is a simple text file that contains information on what the system is, and what should be done. Data sets have names such as "test.mop," "1WDA.mop," "Formaldehyde.mop," "water.dat," "H2O.inp." etc., although for most work the name should be descriptive of what is being done, e.g., "1WDA adding hydrogen atoms.mop" and the suffix should be ".mop" For more information see Examples of Data-Sets.
A job is a single data-set that is run using MOPAC. A job can be simple, e.g., it might optimize the geometry of a molecule, or it might involve two or three calculations, e.g., optimize the geometry of a molecule, then, without stopping, calculate the vibrational frequencies of that molecule. When a geometry calculated in one step is to be used in a subsequent step, OLDGEO is normally used. Only the first calculation requires a geometry to be supplied, all other calculations can either use their own geometry or use that of a previous step.
In MOPAC work, a "calculation" is a simple job, either a stand-alone job, or a single step in a multi-step job. For example, suppose that the first step in a multi-step job is to optimize the geometry of a molecule, and the next step in that job would be to calculate the vibrational frequencies, then the data for the second step would consist of the lines:
appended to the end of the first calculation data set.
A step and a calculation are the same.
Make up a simple data set for ethylene and run it. Name the data set "ethylene.mop" and run it at the command prompt using the command: "C:/program files/MOPAC2016.exe" ethylene.mop (The quotation marks are needed for this command to work.)
In this example, internal coordinates are used, but in protein chemistry Cartesian coordinates are used in almost all jobs.