# Topology error
**URL:** https://gromacs.bioexcel.eu/t/topology-error/7236
**Category:** User discussions
**Tags:** mdrun
**Created:** [September 21, 2023, 7:56am UTC](https://gromacs.bioexcel.eu/t/topology-error/7236 "2023-09-21T07:56:40Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Bisma](https://gromacs.bioexcel.eu/u/Bisma)
#### Post date: [September 21, 2023, 7:56am UTC](https://gromacs.bioexcel.eu/t/topology-error/7236/1 "2023-09-21T07:56:40Z")
GROMACS version:
GROMACS modification: Yes/No
Here post your question
While running the following topology writing command with pdb2gmx for my protein :
gmx pdb2gmx -f 3HTB\_clean.pdb -o 3HTB\_processed.gro -ter
I received following error can anyone help me resolve it
Fatal error: Atom HB3 in residue SER 6 was not found in rtp entry SER with 13 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.
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### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [September 21, 2023, 5:07pm UTC](https://gromacs.bioexcel.eu/t/topology-error/7236/2 "2023-09-21T17:07:26Z")
Have you followed this advice?
> [@Bisma](#):
>
> Option -ignh will ignore all hydrogens in the input.