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
I have checked that the structure files are all in the right path. I don't understand that why Modeller can't read the structure. I notice that the program generated two structure files ( all with xxx_fit) after the alignment. But these "xxx_fit" structures do not include the ligand. If I use these "xxx_fit" structures, there is no error
message saying that "structure not read in", instead, it complain that "One or more atoms absent from MODEL". Since there is no ligand residue in such "xxx_fit" files. And if I manually add the ligand residue into the "xxx_fit", again, the modeller can't read the structure anymore.
I have included the files used for modeling as attachments. I use mod 8v1.
Thank you for help!
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