# Porphyrin protonation state

**URL:** <https://ask.bioexcel.eu/t/porphyrin-protonation-state/2029>\
**Category:** HADDOCK\
**Created:** [May 21, 2020, 8:44am UTC](https://ask.bioexcel.eu/t/porphyrin-protonation-state/2029 "2020-05-21T08:44:16Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![fdeleo](https://avatars.discourse-cdn.com/v4/letter/f/94ad74/32.png) [@fdeleo](https://ask.bioexcel.eu/u/fdeleo)\
**Post date:** [May 21, 2020, 8:44am UTC](https://ask.bioexcel.eu/t/porphyrin-protonation-state/2029/1 "2020-05-21T08:44:16Z")

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Dear all

I’m running Haddock for protein ligand interaction where the ligand is a porphyrin coordinating a Zn2+.

the calculation run finished successfully yet the PRODRG program protonates all the pyrroles within the porph ring. As suggested on the PRODRG server I added a string DELHYD N5 as follows

HETATM 127 H42 UNK 1 0.254 -11.977 -0.082 1.00 0.00 H  
HETATM 128 H43 UNK 1 3.146 -8.757 0.084 1.00 0.00 H  
HETATM 129 H44 UNK 1 4.936 -10.417 0.114 1.00 0.00 H  
DELHYD N5  
DELHYD N6  
DELHYD N7  
DELHYD N8  
TER  
HETATM 21 ZN+2 ZN2 2 -0.089 0.127 0.065 1.00 0.00 Z  
TER  
END

when I test the topology and parameterization of my porph running the prodrg server independently, the server does not add hydrogen on pyrroles, while when I run haddock on the web server keep on protonating the pyrroles.

Can you help me?

many thanks

Federica

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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 21, 2020, 7:25pm UTC](https://ask.bioexcel.eu/t/porphyrin-protonation-state/2029/2 "2020-05-21T19:25:05Z")

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The HADDOCK server is using a local (and older) version of PRODRG.  
This simply won’t work.

If you want to have full control you will have to use a local version of the software and provide your own topology/parameter files.

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**Author:** ![fdeleo](https://avatars.discourse-cdn.com/v4/letter/f/94ad74/32.png) [@fdeleo](https://ask.bioexcel.eu/u/fdeleo)\
**Post date:** [May 21, 2020, 7:28pm UTC](https://ask.bioexcel.eu/t/porphyrin-protonation-state/2029/3 "2020-05-21T19:28:03Z")

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clear. Thank you

on the online version of HADDOCK and the guru account is there a way to load my topol/param files?

best

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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 21, 2020, 7:42pm UTC](https://ask.bioexcel.eu/t/porphyrin-protonation-state/2029/4 "2020-05-21T19:42:34Z")

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No we don’t support upload of topo/param files as there might be too many things going wrong and this would affect the operation/throughput of the portal.  
Sorry.

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**Author:** ![fdeleo](https://avatars.discourse-cdn.com/v4/letter/f/94ad74/32.png) [@fdeleo](https://ask.bioexcel.eu/u/fdeleo)\
**Post date:** [May 22, 2020, 8:17am UTC](https://ask.bioexcel.eu/t/porphyrin-protonation-state/2029/5 "2020-05-22T08:17:06Z")

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ok got it  
thanks a lot