# Fatal error from gmx pdb2gmx

**URL:** <https://gromacs.bioexcel.eu/t/fatal-error-from-gmx-pdb2gmx/7366>\
**Category:** User discussions\
**Created:** [October 11, 2023, 10:55am UTC](https://gromacs.bioexcel.eu/t/fatal-error-from-gmx-pdb2gmx/7366 "2023-10-11T10:55:38Z")\
**Posts on this page:** 1\
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**Author:** ![xave](https://avatars.discourse-cdn.com/v4/letter/x/5fc32e/32.png) [@xave](https://gromacs.bioexcel.eu/u/xave)\
**Post date:** [October 11, 2023, 10:55am UTC](https://gromacs.bioexcel.eu/t/fatal-error-from-gmx-pdb2gmx/7366/1 "2023-10-11T10:55:38Z")

</div>

GROMACS version:2023.2  
GROMACS modification: No  
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 from gmx pdb2gmx 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.

From check\_structure I receive the following:  
PDB id:  
Title:  
Experimental method: unknown  
Resolution (A): N.A.

Num. models: 1  
Num. chains: 2 (A: Protein, B: Protein)  
Num. residues: 422  
Num. residues with ins. codes: 0  
Num. residues with H atoms: 0  
Num. HETATM residues: 5  
Num. ligands or modified residues: 5  
Num. water mol.: 0  
Num. atoms: 3220  
Metal/Ion residues found  
ZN A201  
ZN A202  
ZN B301  
ZN B302  
MG B303  
Running fixside. Options: --fix ALL  
Found no residues with missing or unknown side chain atoms  
Structure not modified, saving due to --force\_save option  
Final Num. models: 1  
Final Num. chains: 2 (A: Protein, B: Protein)  
Final Num. residues: 422  
Final Num. residues with ins. codes: 0  
Final Num. residues with H atoms: 0  
Final Num. HETATM residues: 5  
Final Num. ligands or modified residues: 5  
Final Num. water mol.: 0  
Final Num. atoms: 3220  
Metal/Ion residues found  
ZN A201  
ZN A202  
ZN B301  
ZN B302  
MG B303

Any suggestions to make the MD simulation with the two chains with their ions?

Thanks.

Saverio