Hi everyone,
I want to dock a transition state model at the zinc site of human carbonic anhydrase II and redesign the protein. According to the paper (Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat Chem Biol. 2012 Feb 5;8(3):294-300. doi: 10.1038/nchembio.777.), I use ~/rosetta/tools/zinc_site_redesign module to do my job. Cleaning of PDB was successful, but when I tried to align the protein PDB with my transition state model, error occured:
python align.py -f ~/Downloads/1CA2_clean_A.pdb -l ~/Downloads/TS1-penta.pdb
Traceback (most recent call last):
File "align.py", line 57, in <module>
main()
File "align.py", line 44, in main
sa.generate_alignment_all(METAL,PDB,LIGANDFILE,SUBSTRATEATOMS)
File "/home/aspiration/rosetta/tools/zinc_site_redesign/set_alignment.py", line 70, in generate_alignment_all
self.get_atoms_from_ligand(SUBSTRATEATOMS,LIGANDFILE)
File "/home/aspiration/rosetta/tools/zinc_site_redesign/set_alignment.py", line 101, in get_atoms_from_ligand
tm.write(pdb_lines[i])
KeyError: 'ZN1'
I've checked my PDBs and didn't find any atom called "ZN1". So what's the problem? Thank you for your help.