Re: [modeller_usage] modeling with water, HETATM

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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