# PDB file elemental ion CA without specified charge

**URL:** <https://ask.bioexcel.eu/t/pdb-file-elemental-ion-ca-without-specified-charge/3443>\
**Category:** HADDOCK\
**Created:** [February 3, 2022, 3:19am UTC](https://ask.bioexcel.eu/t/pdb-file-elemental-ion-ca-without-specified-charge/3443 "2022-02-03T03:19:23Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![dawnstar08](https://avatars.discourse-cdn.com/v4/letter/d/bcef8e/32.png) [@dawnstar08](https://ask.bioexcel.eu/u/dawnstar08)\
**Post date:** [February 3, 2022, 3:19am UTC](https://ask.bioexcel.eu/t/pdb-file-elemental-ion-ca-without-specified-charge/3443/1 "2022-02-03T03:19:23Z")

</div>

I input pdb file to calculate binding affinity energy.

but HADDOCK output says  
“Error message  
First pdb file contains an elemental ion CA without specified charge”

I want to modify ion CA’s charge 0 → +2

I tried and look for methods in Pymol. But, I cannot find it.  
Is anyone to teach me to modify charge in Pymol?

Thank you

---

<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:** [February 3, 2022, 8:40am UTC](https://ask.bioexcel.eu/t/pdb-file-elemental-ion-ca-without-specified-charge/3443/2 "2022-02-03T08:40:57Z")

</div>

Check:

```
https://www.bonvinlab.org/software/bpg/

```

and:

```
https://bianca.science.uu.nl/haddock2.4/library

```

PS: And the HADDOCK score is not equal to binding affinity…