stuck

will someone please help me. I would like to use Modeller to align the structures of 41 protein sequences to 1E1E, which has a structure. I have PDB files of all 42 proteins, and I have aligned all of them using ClustalW. I have altered the alignment to the PIR format, as specified. I am trying to perform an initial family alignment of all structures and sequences, as specified in 1.7.2, yet MALIGN3D does not work. It will not read in the structural information. I am very confused by everything and would greatly appreciate if someone could help me go through the process of aligning protein sequences to a known structure.