I'm sorry, but I'm a bit lost.

I understand that English might not be your first language, but you're not doing a very good job of explaining what you need (no offense intended).

This is what I understand from your posts so far:

• You have a number of files with a .pdb extension
• You have a tool that processes these files in some way
• You want to use perl to feed these files to this tool

Now, assuming that the above is correct - I have a couple of questions for you.
Firstly, how do these files need to be passed to your external tool? Do you need to a) just pass the name and location of the file, or b) open the file within perl and then pass it line by line?

And secondly, does this external tool produce any output? And if it does, what should be done with that output?

Perhaps if you can describe as best you can the steps you would take if you were going to process one of these files manually (from start to finish), then that might help me to understand a bit better what it is you need.