Prodigy cannot predict binding affinities for protein-protein by GRAMM-X docking model.

PRODIGY
1

I submitted my PDB file and got the following error.

===========================================================================

command: /usr/local/bin/prodigy model.1_1.pdb --selection A C --temperature 25.0 --contact_list --pymol_selection
exit status: 1
log:
[+] Reading structure file: /data/runs/3QaRoADl/model.1_1.pdb
[+] Parsed structure file model.1_1 (1 chains, 68 residues)
Traceback (most recent call last):
File “/usr/local/bin/prodigy”, line 8, in
sys.exit(main())
File “/usr/local/lib/python3.10/dist-packages/prodigy/predict_IC.py”, line 389, in main
prodigy.predict(
File “/usr/local/lib/python3.10/dist-packages/prodigy/predict_IC.py”, line 152, in predict
self.ic_network = calculate_ic(
File “/usr/local/lib/python3.10/dist-packages/prodigy/predict_IC.py”, line 65, in calculate_ic
raise ValueError(“No contacts found for selection”)
ValueError: No contacts found for selection

I have checked the PDB files with PDB tools and the result is below.

image
image1135×203 7.95 KB

2

Could you visually inspect the complex with (chimera or pymol or vmd) and confirm that chain A is in contact with chain B?

3

I did initial confirmation with Pymol and found that the two proteins actually contracted.

image
image698×489 99.3 KB

4

In your prodigy submission you defined chains A and C… are these correct? From the pymol color coding I would think you are dealing with chains A and B

5

The chains are colored by order (first green, second cyan, etc) not by it’s id.

@Wutthipat1 thanks for checking, if possible could you please send me the input structure for me to run some tests? > rvhonorato@protonmail.com