Error: Radius array is <= 0 for the residue: ILE ,atom: CD

PRODIGY
1

I got this error message when submitting a PDB:

Running Prodigy for structure md_0_1_noPBC
ERROR:
[!] Error when running freesasa:
[!] Error: Radius array is <= 0 for the residue: ILE ,atom: CD

It seems that someone else has similar error previously.

2

The proper atom name should be rather CD1 instead of CD for ILE.

3

Thank you. I have changed the CD to CD1 for ILE.

I also have OT1 and OT2 atoms at the C termini, which causes the same problem Error: Radius array is <= 0 for the residue. How should I modify them?

4

Standard PBD naming (freesasa relies on that and is not our software). I.e. O and OXT

5

Thank you! It works now!

6

what about this error?!

Running Prodigy for structure gsk3b2_complexfit_24
ERROR:
[!] Error when running freesasa:
[!] Error: Radius array is <= 0 for the residue: HIS ,atom: O1P

7

and even O2P and O3P

8

These simply do not belong to a histidine amino acid. Prodigy does not support modified amino acids

9

then what can I do about this?
how should I replace them that doesn’t harm the structure?

10

Again modified amino acids are not supported.

You can delete the phosphate to get some binding affinity estimates, but it will not be the same molecule