Hello! I did molecular dynamics simulation using discovery studio and pulled out my best conformation. I want to run prodigy to see the binding affinity between my protein-protein complex. However, after running it, it doesnt give me any values of delta G or Kd. What can I do to fix this?
Do your proteins have different chainIDs?
Yes I have chain A and chain B. this is always the result I get:
I am also attaching here one of the pdb files for reference.
001.pdb (382.4 KB)
It looks like the culprit are your C terminal oxygens call 1OCT and 2OCT - removing those makes it work.
The command line version does return the following error with your file:
[!] Error when running freesasa:
[!] Error: Radius is <= 0 (-1.0) for the residue: ASN, atom: 1OCT
[!] Make sure the atom names in your PDB file match the canonical naming and belong to default residues
The server should have returned that error too
Thanks for reporting this issue, you should now be able to see the log of prodigy in the result page with further information about the error.