Producing a PDB from a coordinates and topology file

If you have AMBER installed on your workstation, or on a cluster in your home directory (so you have $AMBERHOME set in your enviroment), you can easily produce pdb files from the inpcrd and prmtop files using the AMBER program, ambpdb:

i.e.

$AMBERHOME/exe/ambpdb -p topology-file < coordinates-file > filename.pdb

This effectively uses the topology file to translate the coordinate file into pdb format.