Thank you but I succeed to make model with one ligand but water molecules are not coming in model but putting second single '.'
On Thu, Jan 10, 2013 at 7:17 PM, Modeller Caretaker < firstname.lastname@example.org> wrote:
> 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 > -- > email@example.com http://www.salilab.org/**modeller/http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/**listinfo/modeller_usagehttps://salilab.org/mailman/listinfo/modeller_usage >