# Fatal error: Residue 'EDO' not found in residue topology database

**URL:** <https://gromacs.bioexcel.eu/t/fatal-error-residue-edo-not-found-in-residue-topology-database/5873>\
**Category:** User discussions\
**Created:** [February 25, 2023, 3:21pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-edo-not-found-in-residue-topology-database/5873 "2023-02-25T15:21:30Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![mitykay](https://avatars.discourse-cdn.com/v4/letter/m/ccd318/32.png) [@mitykay](https://gromacs.bioexcel.eu/u/mitykay)\
**Post date:** [February 25, 2023, 3:21pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-edo-not-found-in-residue-topology-database/5873/1 "2023-02-25T15:21:30Z")

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## GROMACS version:2023 GROMACS modification: Yes Here post your question

Program: gmx pdb2gmx, version 2023  
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 616)

Fatal error:  
Residue ‘EDO’ not found in residue topology database

For more information and tips for troubleshooting, please check the GROMACS  
website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)  
Please, someone to guide me . I am having this error.

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**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:** [February 25, 2023, 6:56pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-edo-not-found-in-residue-topology-database/5873/2 "2023-02-25T18:56:56Z")

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Did you visit the link provided in the error message? Or perhaps Google for an answer? You may just find a huge number of useful forum posts :)

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**Author:** ![mitykay](https://avatars.discourse-cdn.com/v4/letter/m/ccd318/32.png) [@mitykay](https://gromacs.bioexcel.eu/u/mitykay)\
**Post date:** [February 27, 2023, 1:27pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-edo-not-found-in-residue-topology-database/5873/3 "2023-02-27T13:27:18Z")

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Yes. I google it out but I couldn’t find a precise answer to this problem in particular.

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**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:** [March 2, 2023, 2:56pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-residue-edo-not-found-in-residue-topology-database/5873/4 "2023-03-02T14:56:38Z")

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You won’t find an exact solution for your exact residue. But the answer is always the same in every post you will find - `pdb2gmx` can only handle species that already exist in force field `.rtp` files. It’s not magic. If you have a nonstandard species, you have to parametrize it yourself or use external (non-GROMACS) programs to write a topology.