# Atom HG in residue SER 25 was not found in rtp entry SER with 11 atoms while sorting atoms

**URL:** <https://gromacs.bioexcel.eu/t/atom-hg-in-residue-ser-25-was-not-found-in-rtp-entry-ser-with-11-atoms-while-sorting-atoms/7293>\
**Category:** User discussions\
**Tags:** pdb2gmx, forcefield\
**Created:** [September 29, 2023, 10:13am UTC](https://gromacs.bioexcel.eu/t/atom-hg-in-residue-ser-25-was-not-found-in-rtp-entry-ser-with-11-atoms-while-sorting-atoms/7293 "2023-09-29T10:13:50Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![Panuwid](https://avatars.discourse-cdn.com/v4/letter/p/dc4da7/32.png) [@Panuwid](https://gromacs.bioexcel.eu/u/Panuwid)\
**Post date:** [September 29, 2023, 10:13am UTC](https://gromacs.bioexcel.eu/t/atom-hg-in-residue-ser-25-was-not-found-in-rtp-entry-ser-with-11-atoms-while-sorting-atoms/7293/1 "2023-09-29T10:13:50Z")

</div>

Hi I have tried using -ter but the result is like this:

Program: gmx pdb2gmx, version 2023.2-Homebrew  
charmm36-jul2022.ff and -ter

Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 870)

Fatal error:

Atom HG in residue SER 25 was not found in rtp entry SER with 11 atoms

while sorting atoms.

For a hydrogen, this can be a different protonation state, or it

might have had a different number in the PDB file and was rebuilt

(it might for instance have been H3, and we only expected H1 & H2).

Note that hydrogens might have been added to the entry for the N-terminus.

Remove this hydrogen or choose a different protonation state to solve it.

Option -ignh will ignore all hydrogens in the input.

For more information and tips for troubleshooting, please check the GROMACS.

website at Common Errors — GROMACS webpage [https://www.gromacs.org](https://www.gromacs.org) documentation

I would like to know how to fix it.  
Thanks You.

Best,  
P

---

<div class="post-metadata">

**Author:** ![Neena](https://avatars.discourse-cdn.com/v4/letter/n/bc79bd/32.png) [@Neena](https://gromacs.bioexcel.eu/u/Neena)\
**Post date:** [September 30, 2023, 1:50am UTC](https://gromacs.bioexcel.eu/t/atom-hg-in-residue-ser-25-was-not-found-in-rtp-entry-ser-with-11-atoms-while-sorting-atoms/7293/2 "2023-09-30T01:50:44Z")

</div>

> [@Panuwid](#):
>
> Atom HG in residue SER 25 was not found in rtp entry SER with 11 atoms
> 
> while sorting atoms.

Did you modify SER 25 residue in PDB file?  
I would check for any discrepancy for atom naming in SER 25, both between your input PDB file and the aminoacids.rtp file for SER.

---

<div class="post-metadata">

**Author:** ![Panuwid](https://avatars.discourse-cdn.com/v4/letter/p/dc4da7/32.png) [@Panuwid](https://gromacs.bioexcel.eu/u/Panuwid)\
**Post date:** [October 1, 2023, 2:19pm UTC](https://gromacs.bioexcel.eu/t/atom-hg-in-residue-ser-25-was-not-found-in-rtp-entry-ser-with-11-atoms-while-sorting-atoms/7293/3 "2023-10-01T14:19:46Z")

</div>

> [@Neena](#):
>
> Did you modify SER 25 residue in PDB file?  
> I would check for any discrepancy for atom naming in SER 25, both between your input PDB file and the aminoacids.rtp file for SER.

I didn’t modify SER 25. How should I fix it?

---

<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [October 1, 2023, 3:28pm UTC](https://gromacs.bioexcel.eu/t/atom-hg-in-residue-ser-25-was-not-found-in-rtp-entry-ser-with-11-atoms-while-sorting-atoms/7293/4 "2023-10-01T15:28:24Z")

</div>

@Panuwid did you follow the link provided in the error message or try `-ignh` as suggested? The solution is quite simple and has been asked and answered hundreds of times. Google is also your friend. You’ll find the answer immediately.