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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
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Getting error with PDB 1A6W #17

Closed mc-robinson closed 3 years ago

mc-robinson commented 6 years ago

For some reason, I am getting an error with PDB 1A6W (unmodified from file downloaded from PDB). This could be on my end, but other proteins seem to working fine.

Thanks, Matt

The relevant error message is included below:

File "/Users/matthewrobinson/bin/propka31", line 11, in load_entry_point('PROPKA==3.1', 'console_scripts', 'propka31')() File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/run.py", line 13, in main File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/molecular_container.py", line 55, in init File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/molecular_container.py", line 110, in extract_groups File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/conformation_container.py", line 41, in extract_groups File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/conformation_container.py", line 146, in setup_and_add_group File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/conformation_container.py", line 155, in init_group File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/group.py", line 356, in setup File "/Users/matthewrobinson/.local/lib/python3.6/site-packages/PROPKA-3.1-py3.6.egg/propka/group.py", line 739, in setup_atoms IndexError: list index out of range

amashaly commented 6 years ago

Any solution to this error yet?

dspencer12 commented 5 years ago

My testing indicates that this issue occurs when atoms are missing in the PDB file (i.e. not resolved by the crystallography experiment). Currently I am working around this issue by using Modeller to fill the missing atom positions.

FloLangenfeld commented 4 years ago

Had the same issue with pdb 1zgl (chains P, R, T and V). Using Modeller solved the issue, indeed. In my case, only OXT atoms at the C-ter residues were missing (which is a quite common feature in X-ray structures).

IMO, the end-user should not be forced to use Modeller, but just be informed that the input structure has something wrong. And it would avoid to add a dependency to propka. A message to the stdout / log should be enough to warn the user that atoms may be missing in the input structure.