I want to include the GDP/GTP and magnesium ions in the threading process for a tubulin homology model I am trying to make (since I do believe this is the ideal way to start formulating the homology model). For some reason, however, only the GTP is included in the output pdb. I get an error message that says:
Error: potential mismatch between sequence from alignment and sequence from PDB!
However, as far as I can tell, the sequence for the template in the alignment is the same as the sequence in the PDB. Here are the associated files, command line input, and error message. Please let me know if there are any other files you need to help solve this problem.