[modeller_usage] ALIGN_CODE

Hello modellers,

I have just started using the programme and have already ran into some difficulty. I am trying to do a homology model .The error message I get suggests that my alignment file does not match my pdb file. Although, all my files are in the same directory as modeller and both written in the same case.

I'm not sure why it is not working? Before running the programme I edited the PDB file using DEEPVIEW to remove the antagonist from the structure. Also I used GENEDOC to produce the alignment and saved it in a PIR format. Not sure if this has something to do with my problem?

attached is my PDB file (called a.pdb), my alignment file (a.pir) and my script file (called script.py) and the log file.

Any help would really be appreciated