On 01/10/2013 01:14 AM, Krupal Jethava wrote: > 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"
We can't tell for sure without seeing your real input files, but by saying "FIRST:@:END ::@" (I think you mean "FIRST:@:END :@:") you are asking Modeller to read all residues from the first chain in the PDB file. So if the ligand and water residues are in a different chain, Modeller won't read them. (Rather than END:@, you could use the residue number and chain ID of the last ligand/water.) Note also that you'll need to set env.io.hetatm=True and env.io.water=True.
Ben Webb, Modeller Caretaker