Error in PDB file. Unknown error: invalid literal for int() with base 10: '2+'

Hello everyone,

I am encountering an error when trying to upload my receptor structure (that has a ZN ion). The zinc ion is properly formatted (last lines of the pdb file below):

TER 1618 SER B 202
HETATM 1619 ZN2+ ZN2 Z 203 25.111 69.456 13.562 1.00 13.00 Z N

What am I missing here? I have uploaded a very similar structure recently and it worked quite well.

I have also uploaded the structure below (renumbered so that it starts from res 1, and sent to pdb_uniquname and pdb_tidy and manually defined the ZN ion format before uploading).

Any help would be greatly appreciated!

Kind regards ,


rec_unq_tidy.pdb (256.0 KB)

Carefully check the column alignment, comparing it to the protein part.

Also if the zinc ion belongs to the protein give it the same chain ID

Thank you for your reply, Prof. Bonvin!

I have modified the chain ID to be identical with the protein (B) and things appear to be properly aligned as far as I can see, but the error persists.

It most likely has to do with the formatting, but it escapes me. Any suggestions?

a mistake staring me in the face: modified the line according to the HADDOCK format (ZN2+ changed to ZN+2), but still did not solve the problem:

HETATM 1618 ZN2+ ZN2 B 203      25.111  69.456  13.562  1.00 13.00          ZN  

ZN2+ should be ZN+2 (if I am correct) :slight_smile:

Thank you, prof. Bonvin, that was indeed the problem!