Problem with running Propka3

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

263 stars 58 forks source link

Problem with running Propka3 #129

Closed AhmedEzat closed 3 years ago

AhmedEzat commented 3 years ago

Dear Sir,

I am not sure if the issue had been raisen before but I get this error while trying to run propka3

Traceback (most recent call last): File "e:\anaconda\lib\runpy.py", line 194, in _run_module_as_main return _run_code(code, main_globals, None, File "e:\anaconda\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "E:\Anaconda\Scripts\propka3.exe__main__.py", line 7, in File "e:\anaconda\lib\site-packages\propka\run.py", line 42, in main my_molecule = read_molecule_file(pdbfile, my_molecule) File "e:\anaconda\lib\site-packages\propka\input.py", line 98, in read_molecule_file conformations, conformation_names = read_pdb( File "e:\anaconda\lib\site-packages\propka\input.py", line 237, in read_pdb for (name, atom) in lines: File "e:\anaconda\lib\site-packages\propka\input.py", line 173, in get_atom_lines_from_pdb model = int(line[6:]) ValueError: invalid literal for int() with base 10: ' \n'

sobolevnrm commented 3 years ago

Can you please provide more information?

What OS and version of Python are you using?
What version of PROPKA are you using?
Can you provide a copy of the PDB file that causes the error?

Thank you

AhmedEzat commented 3 years ago

I am using Windows 10 and python 3.8.8 (Anaconda distribution).

propka3 installed though the command pip install --upgrade propka

Note I tried using propka server https://www.ddl.unimi.it/vegaol/propka.htm and it works with the file but I want to know what is the problem with my installation

AhmedEzat commented 3 years ago

I cannot attach my pdb file and I don't know what is the problem.

intendo commented 3 years ago

@AhmedEzat you may need to zip the file before you attach it.

AhmedEzat commented 3 years ago

model pdb file.docx

sobolevnrm commented 3 years ago

Can you please just add a .txt extension to your PDB file and post it that way? I don't want to introduce additional variables by converting to/from Word. Thanks.

AhmedEzat commented 3 years ago

Model1.txt This is the file.

Thanks for your help

AhmedEzat commented 3 years ago

Is there any solution to my problem?

Many thanks in advance for your efforts.

sobolevnrm commented 3 years ago

Not yet, sorry.

sobolevnrm commented 3 years ago

Hello. Your PDB file appears to be missing an integer for the "MODEL" statement which is required by the standard: https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL