Gap in protein chain and atom naming error

PRODIGY
1

Dear PRODIGY Team and Users,
I am facing the following errors on my protein-protein complex when submitted for PRODIGY analysis. One of my interacting protein has some residues missing due to which i am receiving error and some atom naming errors also. Please let me know how to proceed further and what modifications are required

[!] Structure contains gaps:
B GLY1 < Fragment 0 > B ASN219
A VAL30 < Fragment 1 > A GLN336
A LEU343 < Fragment 2 > A THR664

Running Prodigy for structure vaccine-A-TLR3-B
ERROR:
[!] Error when running freesasa:
[!] Error: Radius array is <= 0 for the residue: ILE ,atom: CD

Thanks in advance.

Best Regards,
Gagandeep Singh

2

The gaps are not the problem. Your atom naming is not consistent with official pdb namings. ILE CD should be CD1here.