ValueError('No contacts found for selection')

PRODIGY
1

I am trying to predict binding affinity of a docked.pdb file ( ligand and receptor) through local prodigy tool, running the following command
prodigy docked.pdb --selection A B
The file has two chains; A that presents the receptor and B that presents the ligand
but i face this error in predict_IC.py file in function calculate_ic
raise ValueError('No contacts found for selection')
I tried to debug the code and found that all_list ( variable in calculate_ic function) has chain A only; nothing presented chain B in the list.
Does any one have a clue what should I search for/do
Thanks

2

Could you please visually inspect your input structure and confirm that chain A has contacts with chain B?

3

And check may-be also the format of your PDB file with our PDB-tools server

4

Thank you for checking my issue and replying.
Do you mean the different formats of structure files like PDB, mmCIF and XML??
What might be the problem of the file format? To what format do you recommend me to convert it

5

Thank you for checking my issue and replying.
Can you guide me to a tool for interactions visualization?

6

I put the hyper link to the file if you prefer to check it. Thank you so much

7

I only recommend to check if your file follows the correct PDB format.

8

Any visualisation software should allow you to check if your molecules are actually in contact. E.g. Chimera, Pymol, …