On Wed, 5 Dec 2007, Mike Kubal wrote: > run_fred "-rec" receptor_file "-dbase" > ligand_file "-prefix" ligand_prefix; In here, take the filenames of each file by saying @filenmame(receptor_file), like this: > run_fred "-rec" @filename(receptor_file) "-dbase" > @filename(ligand_file) "-prefix" ligand_prefix; --