Troubleshooting prodigy results

PRODIGY
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1

Hello Everyone,

I’ve issue. When I analyse the results of my docking with GRAMM-X in PRODIGY to study the molecular interactions, the tool tells me that no contact has been detected. However, visualisation with PyMOL shows me an interaction between the two molecules.

# ===========================================================================
command: prodigy receptor_ligand_model1_1.pdb --selection A X --temperature 25.0 --contact_list --pymol_selection
exit status: 0
log:
[+] Executing 1 task(s) in total
Error processing model: No contacts found for selection
Could you please help me resolve this issue?
Thank you

2

Check that you are specifying the correct chains - they should exist in your PDB file.

Also check that there is not END statement between the chains in the PDB file - should only be a TER statement.