# PDB file error (issue when parsing PDB file)

**URL:** <https://ask.bioexcel.eu/t/pdb-file-error-issue-when-parsing-pdb-file/2199>\
**Category:** HADDOCK\
**Created:** [June 21, 2020, 1:38am UTC](https://ask.bioexcel.eu/t/pdb-file-error-issue-when-parsing-pdb-file/2199 "2020-06-21T01:38:07Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![dpgg94](https://avatars.discourse-cdn.com/v4/letter/d/6de8d8/32.png) [@dpgg94](https://ask.bioexcel.eu/u/dpgg94)\
**Post date:** [June 21, 2020, 1:38am UTC](https://ask.bioexcel.eu/t/pdb-file-error-issue-when-parsing-pdb-file/2199/1 "2020-06-21T01:38:07Z")

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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

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [June 21, 2020, 6:57am UTC](https://ask.bioexcel.eu/t/pdb-file-error-issue-when-parsing-pdb-file/2199/2 "2020-06-21T06:57:49Z")

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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](https://wenmr.science.uu.nl/pdbtools).

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<div class="post-metadata">

**Author:** ![dpgg94](https://avatars.discourse-cdn.com/v4/letter/d/6de8d8/32.png) [@dpgg94](https://ask.bioexcel.eu/u/dpgg94)\
**Post date:** [June 21, 2020, 12:31pm UTC](https://ask.bioexcel.eu/t/pdb-file-error-issue-when-parsing-pdb-file/2199/3 "2020-06-21T12:31:16Z")

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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](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?

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [June 21, 2020, 4:16pm UTC](https://ask.bioexcel.eu/t/pdb-file-error-issue-when-parsing-pdb-file/2199/4 "2020-06-21T16:16:48Z")

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

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**Author:** ![Donia](https://avatars.discourse-cdn.com/v4/letter/d/ac8455/32.png) [@Donia](https://ask.bioexcel.eu/u/Donia)\
**Post date:** [August 16, 2024, 5:50am UTC](https://ask.bioexcel.eu/t/pdb-file-error-issue-when-parsing-pdb-file/2199/5 "2024-08-16T05:50:29Z")

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![Screenshot 2024-08-14 090958](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/6/69eb85b1f5224027b7a8d90b4d1c88bfc41b0662.png)  
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 ?