Filtering energy deposition by particle type using AUXSCORE card

I’ve read considerations which you advised to me. One more thing I want to ask is how filter from for instance all protons every which is not primary one ? IS it possible by using of AUXSCORE card ?

Depend exactly what you want to do.
If your beam is made of proton, than you can profit of the generalized particle BEAMPART, then if you are interested on the fluence you don’t need any AUXSCORE card, which instead you would have to use if you want to a quantity like the deposited energy.
Otherwise, you can use a more powerful tool which is the mgdraw function.

Either way, I’d like to stress again the importance of being aware of the meaningfulness of filtering the energy deposited depending on the type of particle.

I want to do the following. I have stack of targets and beam of protons impact on it. I want to calculate total energy deposited by all primary protons in each of targets. I. e. the summarized energy deposited by all primary protons for instance in cooper target.

Use USRBIN by region, ask for ENERGY as scored quantity, and associate that USRBIN detector to BEAMPART through the AUXSCORE card.
Then, as @amario kept repeating, be aware that the result will depend on the delta (electron) threshold you (even implicitly) set: with a high threshold, several electrons will not be explicitly generated and the corresponding energy deposition will be attributed to the primary proton; with a low threshold, more electrons will be explicitly generated and the corresponding energy deposition will be attributed to them and not to the primary proton.

Should I set the necessary value of threshold via THRESHOLd card ?

One more question is that when run is finished and I press the Process button there are generated .bnn file, but there is no generated .lis file which consists USRBIN card output information. What is the problem ?

The THRESHOLd card has nothing to do with delta electron thresholds, rather is of quite specific use (to inhibit nuclear reactions), as you can read in the manual. The concerned cards are DELTARAY and EMFCUT.
Not sure what you mean with necessary threshold value with respect to your scoring intentions.
Concerning the USRBIN output, there is no problem. Contrary to other scoring cards, in this case Flair plots directly the unformatted .bnn file. If you want to get a human readable output, which is especially the case for region based scoring, you can eventually format it by right-clicking on it in the Files view of the Run tab of Flair (the .bnn file appears under data) and selecting the ‘To ascii’ action, which is automatically invoking the dedicated usbrea post-processing tool. A .lis file will be generated.