# Outputs miss some hydrogen atoms in protein

**URL:** <https://ask.bioexcel.eu/t/outputs-miss-some-hydrogen-atoms-in-protein/2661>\
**Category:** HADDOCK\
**Created:** [November 26, 2020, 3:55pm UTC](https://ask.bioexcel.eu/t/outputs-miss-some-hydrogen-atoms-in-protein/2661 "2020-11-26T15:55:21Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![mieczyslaw](https://avatars.discourse-cdn.com/v4/letter/m/aeb1de/32.png) [@mieczyslaw](https://ask.bioexcel.eu/u/mieczyslaw)\
**Post date:** [November 26, 2020, 3:55pm UTC](https://ask.bioexcel.eu/t/outputs-miss-some-hydrogen-atoms-in-protein/2661/1 "2020-11-26T15:55:21Z")

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It looks like standalone HADDOCK outputs only some hydrogen atoms in protein, the one near the polar groups. This happens even though all hydrogen atoms were present in the input files. This is then an issue when one would like to follow up with some MD calculations where all hydrogen atoms must be present.

Is there a way to make HADDOCK outputting all hydrogen atoms as they were present in the input pdbs?

Thanks.

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**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\
**Post date:** [November 26, 2020, 4:12pm UTC](https://ask.bioexcel.eu/t/outputs-miss-some-hydrogen-atoms-in-protein/2661/2 "2020-11-26T16:12:00Z")

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The parameter you are looking for is `delenph`, in the `run.cns` file

> ```
> {* Remove non-polar hydrogens? *}
> {+ choice: true false +}
> {===>} delenph=true;
> 
> ```

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<div class="post-metadata">

**Author:** ![mieczyslaw](https://avatars.discourse-cdn.com/v4/letter/m/aeb1de/32.png) [@mieczyslaw](https://ask.bioexcel.eu/u/mieczyslaw)\
**Post date:** [November 26, 2020, 5:03pm UTC](https://ask.bioexcel.eu/t/outputs-miss-some-hydrogen-atoms-in-protein/2661/3 "2020-11-26T17:03:01Z")

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Thank you @honoratorv!

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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:** [November 26, 2020, 5:46pm UTC](https://ask.bioexcel.eu/t/outputs-miss-some-hydrogen-atoms-in-protein/2661/4 "2020-11-26T17:46:16Z")

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But it will take more CPU time to keep all non-polar hydrogens.

Simple to add them after HADDOCK, e.g. with hbplus or reduce