[modeller_usage] modeling with water, HETATM

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.