Dear Ben:
Thank you very much for your help.
I fixed the alignment as the way  you suggested. This time, modeller did not complain the structure problem. It went though but stopped later. Here is the error message:
fndatmi_285W> Only      464 residues out of      463 contain atoms of type  CA
delete__442E> One or more atoms absent from MODEL:  O: 454: C: 454: N: 455: CA: 455:
omgdel__425W> Unselected all O C +N +CA dihedrals:      474
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  FE -->  C
              This message is written only for the first such atom.
add_res_442E> One or more atoms absent from MODEL:  NH1:124 O1D:491
I do not quite understand the error message. The ligand in the structure template is "heme". I am not sure if this is the problem. The atom restrains in my .py is based on the residue ID in the template. "NH1:124" is a Arg 124 in the template, "O1D: 491" is the heme ligand. I don't know which part is wrong. Why the modeller says that "one or more atoms absent from MODEL"?
I have included the log file as an attachment. Thank you for your advice!

Modeller Caretaker <> wrote:
Bo Yang wrote:
> 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)
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.

Ben Webb, Modeller Caretaker
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