# Error in making protein topology

**URL:** <https://gromacs.bioexcel.eu/t/error-in-making-protein-topology/10219>\
**Category:** User discussions\
**Created:** [September 23, 2024, 5:22pm UTC](https://gromacs.bioexcel.eu/t/error-in-making-protein-topology/10219 "2024-09-23T17:22:46Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![shanza](https://avatars.discourse-cdn.com/v4/letter/s/4491bb/32.png) [@shanza](https://gromacs.bioexcel.eu/u/shanza)\
**Post date:** [September 23, 2024, 5:22pm UTC](https://gromacs.bioexcel.eu/t/error-in-making-protein-topology/10219/1 "2024-09-23T17:22:46Z")

</div>

I am getting the following error, please help. i am using the command:  
gmx pdb2gmx -f pro.pdb -o pro\_processed.gro -ter -ff charmm36-jul2022 -ignh  
Fatal error:  
Residue 12 named GLN of a molecule in the input file was mapped  
to an entry in the topology database, but the atom CB used in  
that entry is not found in the input file. Perhaps your atom  
and/or residue naming needs to be fixed.

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [September 24, 2024, 8:55am UTC](https://gromacs.bioexcel.eu/t/error-in-making-protein-topology/10219/2 "2024-09-24T08:55:40Z")

</div>

Either there is a missing atom in the PDB file or it is incorrectly named. See [Common errors when using GROMACS - GROMACS 2024.3 documentation](https://manual.gromacs.org/current/user-guide/run-time-errors.html#atom-x-in-residue-yyy-not-found-in-rtp-entry) and [Residue mapped into topology database but atom name not found in file? - #11 by jalemkul](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/11) for more information.