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.
One potential solution to your problem is that you don't need to include the GDP/GTP/Mg in the alignment for the initial threading. Add them after you have generated your initial threaded models (renaming the atoms from HETATM to ATOM), then add a forward slash to the end of your sequence file, and then run rosettaCM.
Derek's method (adding back the ligand after threading) is a good one, but if you want to try threading with the ligand present, what you probably want to try is using the non-annotated sequence in your grishin files. Grishin alignment files take plain one-letter-code sequences, rather than annotated sequences. Remove the parts in square brackets, and I think that should work for you. (Your fasta file will contain the full annotated sequence, but the alignment files should just be the un-annotated one letter codes.)
What's annotated fasta, can you give an example? I tried with and without Z[ligand] as Andrew posted, but none of my ligands made it into the the threaded model. I also have a chain break "/" between my chain, yet the htreaded model is one chain "A". If I remove Z[ligand] as rmoretti suggested, the two chains become fused (they are still 1 chain but fused). How can I add GTP, GDP, MG and TA1 to my fasta sequence?