Prodigy fails to calculate binding energy of protein-protein complex

in the two chain protein complex docked structure (protein1-A, Protein B), prodigy fails with following message

tatus: Failed

Your run failed. Please find below the output of your run which might include an indication about why your run failed :

[!] Structure contains gaps:
A ALA1 < Fragment 0 > A GLY73
A GLY75 < Fragment 1 > A GLU133
A GLN135 < Fragment 2 > A TYR170
A GLY174 < Fragment 3 > A ALA201
B SER24 < Fragment 4 > B CYS281

Running Prodigy for structure BMP1-Szl-complex1
[!] Error when running freesasa:
[!] Error: Radius array is <= 0 for the residue: ILE ,atom: CD

Please anyone can suggest me how the issue can be rectified.

many thanks,

The nomenclature of the ILE atoms is not correct: CD should be CD1 (if I am correct…)

Official PDB namings

is there a way to fix such errors by some program. After fixing ILE CD now I am getting error due to Ala OT1. These pdbs are generated from MD simulation trajectory?

Dear @usharma

We have developed a tool within our pdb-tools package to rename atom names across the different atom name nomenclatures in PDB files. Yet, this tool is under review and is not yet part of the official pdb-tools package. If you are skilled with GitHub you can see the PR here.

Otherwise, for now, you can rename the OT1 name to O using any of your favourite text editors (not Word, but pure text). Please mind that O is followed by two spaced to compensate for the T1. It is likely you will need to modify OT2 also to OXT.

Asap, we integrate our new tool in pdb-tools package we will let you know. If you don’t know pdb-tools please visit →

João T