# Calcium Ion Docking

**URL:** <https://ask.bioexcel.eu/t/calcium-ion-docking/2902>\
**Category:** HADDOCK\
**Created:** [May 1, 2021, 5:23am UTC](https://ask.bioexcel.eu/t/calcium-ion-docking/2902 "2021-05-01T05:23:28Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![help\_me](https://avatars.discourse-cdn.com/v4/letter/h/958977/32.png) [@help\_me](https://ask.bioexcel.eu/u/help_me)\
**Post date:** [May 1, 2021, 5:23am UTC](https://ask.bioexcel.eu/t/calcium-ion-docking/2902/1 "2021-05-01T05:23:28Z")

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I am trying to dock a Calcium ion with my protein, however when I upload the pdb file for the ligand, I keep getting the error: Error in PDB file.  
Issue when parsing the PDB file at line **1**.  
ATOM/HETATM line does not meet the expected format

Below is my PDB file:  
HETATM 1331 CA+2 CA2 A 364 19.958 32.985 27.661 1.00 30.94 Ca  
END

I have browsed other topics related to the same issue, however I am unable to figure out why this error is appearing. Please help me out

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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:** [May 1, 2021, 9:17am UTC](https://ask.bioexcel.eu/t/calcium-ion-docking/2902/2 "2021-05-01T09:17:46Z")

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Check carefully the column alignment - compare it with another pdb file. The format of the PDB files is very strict.

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**Author:** ![help\_me](https://avatars.discourse-cdn.com/v4/letter/h/958977/32.png) [@help\_me](https://ask.bioexcel.eu/u/help_me)\
**Post date:** [May 2, 2021, 7:39am UTC](https://ask.bioexcel.eu/t/calcium-ion-docking/2902/3 "2021-05-02T07:39:44Z")

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I have aligned it with respect to other PDB files and the alignment seems to be fine, however I get the error: DSSP failed to produce an output  
Is there anything else I need to check?

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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:** [May 2, 2021, 8:21am UTC](https://ask.bioexcel.eu/t/calcium-ion-docking/2902/4 "2021-05-02T08:21:21Z")

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Did you define it as a ligand when uploading the molecule?

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**Author:** ![help\_me](https://avatars.discourse-cdn.com/v4/letter/h/958977/32.png) [@help\_me](https://ask.bioexcel.eu/u/help_me)\
**Post date:** [May 2, 2021, 9:19am UTC](https://ask.bioexcel.eu/t/calcium-ion-docking/2902/5 "2021-05-02T09:19:49Z")

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Yes it was defined as ligand

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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:** [May 2, 2021, 9:43am UTC](https://ask.bioexcel.eu/t/calcium-ion-docking/2902/6 "2021-05-02T09:43:56Z")

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Can you please share your input PDB files? Send them directly to us via email.

Note that ion docking is a not a scenario we have been actively supporting.  
But we will check things.