Dear @amrit.p.nayak ,
From my understanding of the description of your problem, you can use the SPECSOUR and GCR-SPE cards to achieve your goal. You can set up the SPECSOUR card by setting the particle injection radius in WHAT(2). You can have a look at section 16.7 of the FLUKA manual for more details.
Given that you are not using the standard FLUKA geometry of the Earth atmosphere, I strongly recommend to use the option NO-NORM in the GCR-SPE card. This option will get rid of the built-in normalization of the Earth atmosphere’s layers and you can always apply the proper normalization in post-process. Please note that for running the simulation with the NO-NORM option, a folder called gcr must be present in the folder where you run your simulation: the grc folder must contains all the *.spc, renamed as follows:
01NO-NORM.spc
02NO-NORM.spc
03NO-NORM.spc
...
Other physics/transport cards will mainly depend on your physics problem.
Finally, for GCR applications make sure you link your executable to DPMJET.
Cheers,
Angelo