Hello,
Thank you for posting your code - nice work!
I have installed and tested, with success, a few of the sample pocket pdbs.
When trying to generate my own pocket pdb files, I run into the following error:
PocketFlow# python create_pocket_pdb.py --protein test.pdb --ligand test_lig.sdf
PyMOL not running, entering library mode (experimental)
Traceback (most recent call last):
File "create_pocket_pdb.py", line 32, in
main()
File "create_pocket_pdb.py", line 25, in main
pocketblock, = SplitPocket._split_pocket_with_surface_atoms(
File "/PocketFlow/pocket_flow/utils/process_raw.py", line 68, in _split_pocket_with_surface_atoms
protein.compute_surface_atoms()
File "/PocketFlow/pocket_flow/utils/ParseFile.py", line 480, in compute_surface_atoms
res.atom_dict[a.name].is_surf = True
KeyError: 'OG1'
Hello, Thank you for posting your code - nice work! I have installed and tested, with success, a few of the sample pocket pdbs. When trying to generate my own pocket pdb files, I run into the following error:
PocketFlow# python create_pocket_pdb.py --protein test.pdb --ligand test_lig.sdf PyMOL not running, entering library mode (experimental) Traceback (most recent call last): File "create_pocket_pdb.py", line 32, in
main()
File "create_pocket_pdb.py", line 25, in main
pocketblock, = SplitPocket._split_pocket_with_surface_atoms(
File "/PocketFlow/pocket_flow/utils/process_raw.py", line 68, in _split_pocket_with_surface_atoms
protein.compute_surface_atoms()
File "/PocketFlow/pocket_flow/utils/ParseFile.py", line 480, in compute_surface_atoms
res.atom_dict[a.name].is_surf = True
KeyError: 'OG1'
Any help is appreciated.