# Error while running writing the topology

**URL:** <https://gromacs.bioexcel.eu/t/error-while-running-writing-the-topology/6438>\
**Category:** User discussions\
**Tags:** pdb2gmx, forcefield, mdp-parameters, mdrun, analysis-tools\
**Created:** [May 18, 2023, 10:54am UTC](https://gromacs.bioexcel.eu/t/error-while-running-writing-the-topology/6438 "2023-05-18T10:54:58Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![sreeshma\_raj](https://avatars.discourse-cdn.com/v4/letter/s/439d5e/32.png) [@sreeshma\_raj](https://gromacs.bioexcel.eu/u/sreeshma_raj)\
**Post date:** [May 18, 2023, 10:54am UTC](https://gromacs.bioexcel.eu/t/error-while-running-writing-the-topology/6438/1 "2023-05-18T10:54:58Z")

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GROMACS version: 2023.1  
GROMACS modification: Yes/No  
Here post your question

I have one protein and ligand for simulation. am using charmm forcefield. when i run the command for topolgy generation:

gmx pdb2gmx -f complex\_aca.pdb -o protein\_aca.gro -ter

it showed the following error:  
Fatal error:  
The residues in the chain PCA1–LEU496 do not have a consistent type. The  
first residue has type ‘Other’, while residue TYR2 is of type ‘Protein’.  
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.

someone please help me to solve this issue.

thank you in advance.

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**Author:** ![dlakhan](https://avatars.discourse-cdn.com/v4/letter/d/ecc23a/32.png) [@dlakhan](https://gromacs.bioexcel.eu/u/dlakhan)\
**Post date:** [June 18, 2024, 1:54am UTC](https://gromacs.bioexcel.eu/t/error-while-running-writing-the-topology/6438/2 "2024-06-18T01:54:03Z")

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Heyy, my name is Dharati

Now I am studying on GROMACS for only protein and tried to generate topology file with amber force field but it is showing this type of error  
Fatal error:  
The residues in the chain LYS1–LEU129 do not have a consistent type. The  
first residue has type ‘Protein’, while residue ALA9 is of type ‘Other’.  
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.

So, if you know then can you help me to solve this error???

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**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:** [June 18, 2024, 7:23am UTC](https://gromacs.bioexcel.eu/t/error-while-running-writing-the-topology/6438/3 "2024-06-18T07:23:17Z")

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Please, don’t ask the same question in multiple threads. Wait a few days to see if you get any answers in the first thread you posted: [Fatal error while doing Protein-ligand simulation using GROMACS 2023 - #5 by dlakhan](https://gromacs.bioexcel.eu/t/fatal-error-while-doing-protein-ligand-simulation-using-gromacs-2023/7515/5).