Hi,I am a new Rosetta learner, just following the protein protein docking tutorials to study now.
In the protein preparation step, an error turned up as follows:
$ python ~/rosetta_scripts/scripts/clean_pdb.py complex.pdb ignorechain
Looking for: complex.pdb
Found preoptimised or otherwise fixed PDB file.
Traceback (most recent call last):
File "/home_soft/home/simm05/rosetta_scripts/scripts/clean_pdb.py", line 156, in ?
if (chainid == line or ignorechain or removechain):
IndexError: string index out of range
1. I wonder if there is anything wrong with my pdb? I just put 2 docking proteins in 1 pdb file, removed waters and hydrogens, and named them as two chains.
2. Is there any certain requirments about the pdb file?
3. One protein lacks the structure of 22 amino acid , its structure is broken in two. Does it affect the docking process? Do I need to add its structural information by homology modeling or something?
4. Does existing of small molecule ligands affect docking？
Thanks a lot!