# Error: elemental ion CA without specified charge

**URL:** <https://ask.bioexcel.eu/t/error-elemental-ion-ca-without-specified-charge/347>\
**Category:** HADDOCK\
**Created:** [April 20, 2017, 11:05am UTC](https://ask.bioexcel.eu/t/error-elemental-ion-ca-without-specified-charge/347 "2017-04-20T11:05:51Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![lhutten](https://avatars.discourse-cdn.com/v4/letter/l/c6cbf5/32.png) [@lhutten](https://ask.bioexcel.eu/u/lhutten)\
**Post date:** [April 20, 2017, 11:05am UTC](https://ask.bioexcel.eu/t/error-elemental-ion-ca-without-specified-charge/347/1 "2017-04-20T11:05:51Z")

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I am using Haddock to make a complex of RAP and LDLR (I am aware that there is an existing complex, however I want to see if I can dock these two together before I dock apoE to LDLR)

I get the error that my CA ions (I’ve got 8 in my file for LDLR (1N7D) are without specified charge so I defined them like this (I’ve also tried other LDLR files but those get the same error.):

original:  
HETATM 4822 CA CA A1008 21.696 63.631 -4.419 1.00124.70 CA

how I defined it:  
HETATM 4822 CA+2 CA2 A1008 21.696 63.631 -4.419 1.00124.70 CA

However when I define the ions like this I get another error:  
pdb file is incorrectly formatted. Please align the columns of your PDB properly.

I’ve tried to fix this by using the Protein Database File Editor instead of just fixing it in an txt file, but I still get this error.  
I’ve also tried to remove the 8 CA atoms that I have but the same arror occurs

My supervisor suggested to compare this file to another file from last year that did work (4U7T) (it contained a Zn ion instead of CA), however the ions are defined the same way, so without any charge.

If anyone knows a solution that would make me really happy!

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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:** [April 20, 2017, 1:48pm UTC](https://ask.bioexcel.eu/t/error-elemental-ion-ca-without-specified-charge/347/2 "2017-04-20T13:48:59Z")

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You must have shifted some columns in your PDB when editing it. Correct this.

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**Author:** ![mtrellet](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/mtrellet/32/42_2.png) [@mtrellet](https://ask.bioexcel.eu/u/mtrellet)\
**Post date:** [April 21, 2017, 7:23am UTC](https://ask.bioexcel.eu/t/error-elemental-ion-ca-without-specified-charge/347/3 "2017-04-21T07:23:22Z")

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You can try our PDB format checking tool available here: [https://github.com/haddocking/pdb-tools](https://github.com/haddocking/pdb-tools)

It is named `pdb_format.py` and detect most of the obvious errors that can sneak into a PDB file.

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<div class="post-metadata">

**Author:** ![lhutten](https://avatars.discourse-cdn.com/v4/letter/l/c6cbf5/32.png) [@lhutten](https://ask.bioexcel.eu/u/lhutten)\
**Post date:** [April 21, 2017, 3:34pm UTC](https://ask.bioexcel.eu/t/error-elemental-ion-ca-without-specified-charge/347/4 "2017-04-21T15:34:09Z")

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Thank you! I used the pdb\_striphet.py script to get the CA atoms out in the end and now my run is in the queue