I am trying to make model with Ligand (37 HetAtom) and 3 water molecule. I used the same script as in manual but getting the error that 

"Number of residue in alignment and pdb are different: 324      288 for alignment entry: tseq.pdb"

In My alignment file: 

1) query seq = 296 (residues) 

2) pdb = 287 (residues) + 3 (water HETATM) + ligand (34 HETATM)

align-ligand.ali has