# Generating ion.tpr file

**URL:** <https://gromacs.bioexcel.eu/t/generating-ion-tpr-file/7525>\
**Category:** User discussions\
**Created:** [November 1, 2023, 11:49am UTC](https://gromacs.bioexcel.eu/t/generating-ion-tpr-file/7525 "2023-11-01T11:49:03Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![AF1](https://avatars.discourse-cdn.com/v4/letter/a/eada6e/32.png) [@AF1](https://gromacs.bioexcel.eu/u/AF1)\
**Post date:** [November 1, 2023, 11:49am UTC](https://gromacs.bioexcel.eu/t/generating-ion-tpr-file/7525/1 "2023-11-01T11:49:03Z")

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Hi

I am getting the following error from Lysozyme in water tutorial. I successfully completed this tutorial a few months ago but this week it seems the file gets broken at the ions.tpr output step. Please see message and file generated.

Command line:  
gmx grompp -f ions.mdp -c 1AKI\_solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry ‘ns\_type’

NOTE 1 [file ions.mdp]:  
With Verlet lists the optimal nstlist is \>= 10, with GPUs \>= 20. Note  
that with the Verlet scheme, nstlist has no effect on the accuracy of  
your simulation.

Setting the LD random seed to -471713371  
Generated 330891 of the 330891 non-bonded parameter combinations  
Generating 1-4 interactions: fudge = 0.5  
Generated 330891 of the 330891 1-4 parameter combinations  
Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_A’  
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 18409]:  
System has non-zero total charge: 8.000000  
Total charge should normally be an integer. See  
[Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic)  
for discussion on how close it should be to an integer.

Analysing residue names:  
There are: 129 Protein residues  
There are: 10644 Water residues  
Analysing Protein…  
Number of degrees of freedom in T-Coupling group rest is 69741.00

NOTE 3 [file ions.mdp]:  
You are using a plain Coulomb cut-off, which might produce artifacts.  
You might want to consider using PME electrostatics.

This run will generate roughly 3 Mb of data

There were 3 notes

 ![Screenshot from 2023-11-01 13-48-27](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/7/736da25f432f4f6725bdbd004843fda76f855275.png)

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**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [November 2, 2023, 3:24pm UTC](https://gromacs.bioexcel.eu/t/generating-ion-tpr-file/7525/2 "2023-11-02T15:24:06Z")

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Hi,

What makes you think the file is broken, does the next step involving `gmx genion` fail? The .tpr is a binary file so it’s not supposed to be human-readable, and your `gmx grompp` output seems just fine.

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<div class="post-metadata">

**Author:** ![AF1](https://avatars.discourse-cdn.com/v4/letter/a/eada6e/32.png) [@AF1](https://gromacs.bioexcel.eu/u/AF1)\
**Post date:** [November 2, 2023, 6:41pm UTC](https://gromacs.bioexcel.eu/t/generating-ion-tpr-file/7525/3 "2023-11-02T18:41:32Z")

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Hi yes thank you so much. I successfully completed the tutorial and got the right graphs at the end. Thank you I did not know the files were meant to be binary.