# Is pH or protonation states considered in Prodigy?

**URL:** <https://ask.bioexcel.eu/t/is-ph-or-protonation-states-considered-in-prodigy/3737>\
**Category:** PRODIGY\
**Created:** [May 27, 2022, 8:49am UTC](https://ask.bioexcel.eu/t/is-ph-or-protonation-states-considered-in-prodigy/3737 "2022-05-27T08:49:29Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![lanselibai](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lanselibai](https://ask.bioexcel.eu/u/lanselibai)\
**Post date:** [May 27, 2022, 8:49am UTC](https://ask.bioexcel.eu/t/is-ph-or-protonation-states-considered-in-prodigy/3737/1 "2022-05-27T08:49:30Z")

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Can I ask if pH or protonation states can be considered to perform the Prodigy? e.g. if I supply the PDB with different hydrogens and all the same heavy atoms, would the results be different?

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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 27, 2022, 11:13am UTC](https://ask.bioexcel.eu/t/is-ph-or-protonation-states-considered-in-prodigy/3737/2 "2022-05-27T11:13:29Z")

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No it is not - only heavy atoms are considered