If you are going through the other person's (the at-fault party) property damage insurance then you will not be responsible for a deductible. You will just need to agree with the insurance company's claim adjuster on a settlement amount for your totaled out vehicle.

If instead you put the claim through your own collision coverage then yes, the deductible amount is due and will likely be taken out of the settlement amount for the vehicle. You may see if your insurance company plans to subrogate with the other party's insurance company. If so then you may ask if they will be able to recover your deductible amount during this subrogation process.