Subject: Re: [modeller_usage] modeling with water, HETATM
From: Modeller Caretaker <>
Date: Thu, 10 Jan 2013 11:17:32 -0800
Cc:
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.