# Atom HD1 in residue HIS was not found in rtp entry HSE with 17 atoms while sorting atoms

**URL:** <https://gromacs.bioexcel.eu/t/atom-hd1-in-residue-his-was-not-found-in-rtp-entry-hse-with-17-atoms-while-sorting-atoms/9512>\
**Category:** User discussions\
**Tags:** pdb2gmx\
**Created:** [June 25, 2024, 8:14pm UTC](https://gromacs.bioexcel.eu/t/atom-hd1-in-residue-his-was-not-found-in-rtp-entry-hse-with-17-atoms-while-sorting-atoms/9512 "2024-06-25T20:14:04Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![nooraaz](https://avatars.discourse-cdn.com/v4/letter/n/5f8ce5/32.png) [@nooraaz](https://gromacs.bioexcel.eu/u/nooraaz)\
**Post date:** [June 25, 2024, 8:14pm UTC](https://gromacs.bioexcel.eu/t/atom-hd1-in-residue-his-was-not-found-in-rtp-entry-hse-with-17-atoms-while-sorting-atoms/9512/1 "2024-06-25T20:14:04Z")

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GROMACS version: 2022  
GROMACS modification: No

I’m using pdb2gmx to create a topology for my protein. I get an error for HIS residue. I know it’s because of the protonation state, and what I have in my pdb is HSD. I’m just wondering why it doesn’t automatically map HIS with all HSE/HSE/HSP residues, to see which one fits it. How do you deal with this issue?

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [June 25, 2024, 8:19pm UTC](https://gromacs.bioexcel.eu/t/atom-hd1-in-residue-his-was-not-found-in-rtp-entry-hse-with-17-atoms-while-sorting-atoms/9512/2 "2024-06-25T20:19:53Z")

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Which forcefield you are using? you can change the protonation state using appropriate flag from gmx pdb2gmx

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**Author:** ![nooraaz](https://avatars.discourse-cdn.com/v4/letter/n/5f8ce5/32.png) [@nooraaz](https://gromacs.bioexcel.eu/u/nooraaz)\
**Post date:** [June 25, 2024, 8:39pm UTC](https://gromacs.bioexcel.eu/t/atom-hd1-in-residue-his-was-not-found-in-rtp-entry-hse-with-17-atoms-while-sorting-atoms/9512/3 "2024-06-25T20:39:17Z")

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I’m using charmm27. which flag should I use?