If your .pbp file is an official game purchased from the PlayStation Store, it is likely encrypted. Standard tools like PSX2PSP cannot extract these directly. You would first need to use a tool like to decrypt the official PBP before you can extract and patch the ISO.
To create a patched ISO file, you'll need to use a tool like UltraISO or ImgBurn. Here's a general outline of the process:
Community members often discuss the trade-offs between using PBP for convenience versus ISO for compatibility: