# Pdb2gmx fatal error: residue naming

**URL:** <https://gromacs.bioexcel.eu/t/pdb2gmx-fatal-error-residue-naming/9124>\
**Category:** User discussions\
**Created:** [May 10, 2024, 1:18pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-fatal-error-residue-naming/9124 "2024-05-10T13:18:53Z")\
**Posts on this page:** 1\
**Showing post:** 5

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**Author:** ![ivangreg](https://avatars.discourse-cdn.com/v4/letter/i/7993a0/32.png) [@ivangreg](https://gromacs.bioexcel.eu/u/ivangreg)\
**Post date:** [May 14, 2024, 4:28pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-fatal-error-residue-naming/9124/5 "2024-05-14T16:28:09Z")

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Hi @scinikhil

If my memory serves me right, that is the top hit that I got doing a search to try to solve this kind of problem.

Could you please do the community, @kj655, and me a favour?

Within that post (that is 17 years old) or any other post:  
**Could you please specifically point to the solution?**  
(Not the description of the problem but the solution.)

It seems that knowledgeable scientists over the years have found this atom-naming incompatibility a challenging problem. See for instance [this](https://gromacs.bioexcel.eu/t/charmm36-to-gromacs-porting/2101) 2021 exchange between @awacha and @jalemkul .

My understanding is that that very conversation lead to a [2023 publication](https://doi.org/10.1021/acs.jcim.3c00860) by those two scientists.

The solution proposed in that paper points to a [converter](https://gitlab.com/awacha/charmm2gmx) on a GitLab page. Unfortunately, the README.md in GitLab says only this:

"  
Note: This is work in progress. Do not use this code, not even at your own  
risk! The resulting force field is not guaranteed to be correct at all.

On-line documentation: [https://awacha.gitlab.io/charmm2gmx](https://awacha.gitlab.io/charmm2gmx)  
"

In conclusion, for over 17 years people have been reporting this problem. If you could show a documented solution, I and many others would be profoundly grateful to you.

Ivan

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