Problem with running Propka3

[AhmedEzat]

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]

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]

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]

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

[intendo]

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

[AhmedEzat]

model pdb file.docx

[sobolevnrm]

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]

Model1.txt
This is the file.

Thanks for your help

[AhmedEzat]

Is there any solution to my problem?

Many thanks in advance for your efforts.

[sobolevnrm]

Not yet, sorry.

[sobolevnrm]

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