Getting an error while running

1

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command: prodigy .pdb --selection A B --temperature 25.0 --contact_list --pymol_selection
exit status: 1
log:
[+] Reading structure file: /data/runs/3Y69CXxm/.pdb
[!] Structure ‘’ could not be parsed
Traceback (most recent call last):
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/parsers.py”, line 158, in parse_structure
s = sparser.get_structure(sname, path)
File “/usr/local/lib/python3.10/site-packages/Bio/PDB/PDBParser.py”, line 99, in get_structure
raise ValueError(“Empty file.”)
ValueError: Empty file.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/usr/local/bin/prodigy”, line 8, in
sys.exit(main())
File “/usr/local/lib/python3.10/site-packages/prodigy/predict_IC.py”, line 414, in main
structure, n_chains, n_res = parse_structure(struct_path)
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/parsers.py”, line 161, in parse_structure
raise Exception(exeption)
Exception: Empty file.

2

Looks like you have a typo in the PDB path/filename… Is the / before .pdb correct?

3

No, I don’t think so. The file name is ywahz.pdb.
Actually, I have another question. Is it possible to upload the AlphaFold multimer output which has two proteins. Can we find the binding affinity of those output?

4

That’s not what the error message shows… check again