Dear,
  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
>P1;tseq.pdb
structureX:tseq.pdb:FIRST:@:END  ::@:::
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA.....
................................*

>P1;qseq
sequence:qseq:FIRST:@:END  ::@:::
AAAAAAAAAAA--AAAAAAAAAAAAAAAAAAA.....
................................*

I am using Modeller9v7 and python2.5.1

I will be very thankful for your help.