PDB file error (issue when parsing PDB file)

HADDOCK
1

Error:Error in PDB file.
Issue when parsing the PDB file at line 9 .
X,Y,Z coordinates, occupancy, and temperature (b) factors must be decimal numbers.

I got this error above when sending a protein structure for protein-protein docking.
Have looked at line 9 but i am not sure what error to look out for.
Could anyone teach me what went wrong with Line 9?
I’ve copied the few lines below.
Thanks!

ATOM 6 H2 ASP A 2 -19.038 -46.695 -10.990 1.00 15.00 H
ATOM 7 H3 ASP A 2 -18.024 -46.558 -9.673 1.00 15.00 H
ATOM 8 H ASP A 2 -17.671 -44.583 -10.937 1.00 H
ATOM 9 CB ASP A 2 -19.700 -44.039 -11.237 1.00 20.00 C

2

The PDB format is strict and column formatted. If you mess up the columns you mess up the coordinates…
Look at at file taken from the PDB and compare if the column are aligned with your file.

You can also check for problems with our PDB-Tools, now available as web server at:

https://wenmr.science.uu.nl/pdbtools.

3

ah i see… Is there an automated way to align the columns?

I’ve checked the structure using pdb_validate and got this output below:

[!] Line 2529 is long: 81 > 80
[!] Line 7467 is long: 81 > 80
[!] Line 9995 is long: 81 > 80
[!] Line 14926 is long: 81 > 80
[!] Line 14927 is short: 3 < 80

Not sure what it means as i couldn’t find info on it from this page: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM

Can i check with you if i have used the correct block for validating the PDB file?

4

May-be try reading it in pymol for example and exporting the file again as a PDB file.

5

Screenshot 2024-08-14 090958
what dose
mean here?i’ve checked pdb file for any errors and i didn’t find ?if this symbol means something wrong how can i solve it ?