> The PDB file I_m using as a template starts at residue > 8 and ends at residue 315. So, my alignement is as > follows:
You should check in the PDB file whether there are any additional (or missing) residues, so while the numbering may go from 8 to 315 for the ATOM entries, the sequence is shorter or longer (longer due to alternate residue positions, perhaps, but this is unlikely). You should also check the chain code for the PDB - if it is not blank (ie a letter between the residue name code and residue number) then you need to put the correct chain code in the structureX entry. From the numbers after the error message (309 0), it looks like *no* PDB file residues were read in, which suggests a problem with the chain code (or no residue number 8 at the beginning).
there are more things to check, but these are the basics! j.