Hi
I would like to know how I can add H atoms to my ligand, ADP in the protein complex.
I was trying to add H atoms to one of my ligand, ADP.
When I types "phenix.elbow --final-geometry=test10bcoot_h_refine_001.pdb --residue=ADP --output=model_h",
it went on but failed with the following error message:
Traceback (most recent call last):
File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1201, in <module>
run()
File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1108, in run
molecule = post_process(molecule, options)
File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 577, in post_process
options,
File "/home2/yjcho/phenix-1.3-final/elbow/elbow/utilities/optimisation_manager.py", line 331, in optimisation_manager
pre_opt))
File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 857, in WritePDB
original_order=original_order,
File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 965, in WritePDB2String
self.AdjustHydrogenNames()
File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 940, in AdjustHydrogenNames
if test_name[3]==" ": test_name[3]="0"
TypeError: 'str' object does not support item assignment
FYI. ADP is names as ADP as a residue name in the pdb file but has different chain names.
By the way, I should mention that I used phenix.reduce first for adding H atoms but it was not able to add sugar H's in ADP molecule albeit other residues were fine.
Thanks in advance for your help.
Best,
YoungJin
