# Pdb2gmx says a H is missing from the rtp entry but is not present in pdb

**URL:** https://gromacs.bioexcel.eu/t/pdb2gmx-says-a-h-is-missing-from-the-rtp-entry-but-is-not-present-in-pdb/13291
**Category:** User discussions
**Created:** [March 9, 2026, 8:18am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-says-a-h-is-missing-from-the-rtp-entry-but-is-not-present-in-pdb/13291 "2026-03-09T08:18:01Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![johannekuhr](https://avatars.discourse-cdn.com/v4/letter/j/45deac/32.png) [@johannekuhr](https://gromacs.bioexcel.eu/u/johannekuhr)
#### Post date: [March 9, 2026, 8:18am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-says-a-h-is-missing-from-the-rtp-entry-but-is-not-present-in-pdb/13291/1 "2026-03-09T08:18:01Z")

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GROMACS version: 2023.3-Ubuntu\_2023.3\_1ubuntu3  
GROMACS modification: Yes/No  
Hi  
I get this message when trying to run pdb2gmx: Atom H in residue TYR 2 was not found in rtp entry TYR with 21 atoms while sorting atoms.  
No matter what peptide I try it always says there is a H in residue 2 that is not found in the rtp file, but there is no atom in the pdb file in residue 2 that is just called H, så I don’t know what to do about it. When I try to use -ignh it says segmentatin fault (core dumped), so that doesn’t fix it. Hope someone know what to do  
PS. I am pretty new at this, so doesn’t know a lot