I try to model the ligand into my model by following the example of
"Tutorial-2: Modeling ligands in the binding site'. First, I use a
template and one of my model to build a alignment of the two. Then
manually change the alignment to add "/.." to the end of the structures
and sequence in the alignment. And change the number of residues of the
structure file in the alignment. I then do the modeling using the
modified alignment. But I keep getting the error message:
modeller. error: check_a_337E> structure not read in
If you use Modeller 8v2 or later, you will get a printout of the
sequence mismatch which will help you here. I ran your script and got:
read_te_290E> Number of residues in the alignment and pdb files are
different: 465 464
For alignment entry: 1 1PQ2-2C8Ahem
x (mismatch at alignment position 465)
Alignment VTKGIVSLPPSYQICFIPV..
PDB VTKGIVSLPPSYQICFIPVh
Match ********************
i.e. your alignment lists two BLK residues, but your PDB structure
contains only one HETATM residue (a heme group). So just remove one '.'
from your alignment file (both for the template and the target
sequence). I would also suggest that you remove the chain break (/)
since in your input PDB the ligand is in the same chain (A) as the amino
acids, while the chain break would force your model to put the ligand in
a separate chain.