With PATRAN you can select what groups you want to include in the analysis deck. So, a good way to do what you seem to be wanting to do is to build groups representing the different element combinations you want to analyze. When you set up your analysis runs, you can specify which groups you'd like to write to the analysis deck. You can control what loads and constraints you include with the load case options. You'll still have to create a separate analysis deck for each combination of elements, but you can do it all from one PATRAN db.
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