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.
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
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 < modeller-care@salilab.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 > -- > modeller-care@salilab.org 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 >
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Krupal Jethava -
Modeller Caretaker