# Problem with Fatal error from gmx pdb2gmx in the Protein MD Setup wf

**URL:** <https://ask.bioexcel.eu/t/problem-with-fatal-error-from-gmx-pdb2gmx-in-the-protein-md-setup-wf/4600>\
**Category:** BioBB\
**Created:** [October 11, 2023, 9:40am UTC](https://ask.bioexcel.eu/t/problem-with-fatal-error-from-gmx-pdb2gmx-in-the-protein-md-setup-wf/4600 "2023-10-11T09:40:05Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![saverio](https://avatars.discourse-cdn.com/v4/letter/s/dbc845/32.png) [@saverio](https://ask.bioexcel.eu/u/saverio)\
**Post date:** [October 11, 2023, 9:40am UTC](https://ask.bioexcel.eu/t/problem-with-fatal-error-from-gmx-pdb2gmx-in-the-protein-md-setup-wf/4600/1 "2023-10-11T09:40:05Z")

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HI,  
I should like to adapt the “Protein MD Setup tutorial using BioExcel Building Blocks” workflow  
to the protein of my concern including the Zn and Mg ions present in the solved structure.  
HI,  
I should like to adapt the “Protein MD Setup tutorial using BioExcel Building Blocks” workflow  
to the protein of my concern including the Zn and Mg ions present in the solved structure.  
I have used different ff ( amber99, amber99sd, amber99sd-idln ,oplsaa ).  
The problem is that I receive the following:

“Fatal error:  
The residues in the chain ALA1–ZN202 do not have a consistent type. The first  
residue has type ‘Protein’, while residue ZN201 is of type ‘Ion’. Either there  
is a mistake in your chain, or it includes nonstandard residue names that have  
not yet been added to the residuetypes.dat file in the GROMACS library  
directory. If there are other molecules such as ligands, they should not have  
the same chain ID as the adjacent protein chain since it’s a separate  
molecule.”

The solved structure has two chains.  
The error is for the first chain having only Zns coordinated  
by 4 Cys and 3 Cys and 1 His for the first and second ion respectively.  
The second chain has two Zns, coordinated by Cys and His and one MG.  
My concern is for the MG that is coordinated by an Asp and Glu in an active site.  
Some papers refer that the previous residues together with other two Asp and Glu are catalytic residues.  
I am new to GROMACS.  
Any suggestions to make the MD simulation with the two chains with their ions?

Thanks.

Saverio

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<div class="post-metadata">

**Author:** ![genis.bayarri](https://avatars.discourse-cdn.com/v4/letter/g/6bbea6/32.png) [@genis.bayarri](https://ask.bioexcel.eu/u/genis.bayarri)\
**Post date:** [October 11, 2023, 10:01am UTC](https://ask.bioexcel.eu/t/problem-with-fatal-error-from-gmx-pdb2gmx-in-the-protein-md-setup-wf/4600/2 "2023-10-11T10:01:13Z")

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Hi Saverio,

It seems that this error is related to GROMACS, not to the BioExcel Building Blocks.

Please take a look to the GROMACS forum:

> **[GROMACS forums](https://gromacs.bioexcel.eu/)**
>
> GROMACS community forums supported by BioExcel, the European Centre of Excellence for Computational Biomolecular Research.

Best.

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<div class="post-metadata">

**Author:** ![xave](https://avatars.discourse-cdn.com/v4/letter/x/5fc32e/32.png) [@xave](https://ask.bioexcel.eu/u/xave)\
**Post date:** [October 11, 2023, 10:02am UTC](https://ask.bioexcel.eu/t/problem-with-fatal-error-from-gmx-pdb2gmx-in-the-protein-md-setup-wf/4600/3 "2023-10-11T10:02:27Z")

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Ok.

Thanks.

Saverio