Where to start?
in reply to Reading PDB files
First, I would really suggest the book Learning Perl, authored by our very own merlyn.
Next, get yourself to CPAN, the Comprehensive Perl Archive Network. There are literally thousands of useful Perl modules for doing all sorts of things, like reading special file formats and working with other programs. Since you are probably using Perl on Windows, and therefore you probably have Activestate Perl, you will want to learn how to use PPM to install those modules on your machine.
Finally, if by PDB file you are referring to a Protein Data
Base Bank file, you will want to check out BioPerl, which has many useful bioinformatics functions, including reading special file formats. You might also want to consider gettting Beginning Perl for Bioinformatics, which is a pretty good reference for a scientist who wants to learn bioinformatics.
Good luck, and feel free to come back with more specific questons when you've started writing code.
Project coordinator of the Generic Model Organism Database Project