# Error in user input: Required option was not provided, and the default file 'topol' does not exist

**URL:** <https://gromacs.bioexcel.eu/t/error-in-user-input-required-option-was-not-provided-and-the-default-file-topol-does-not-exist/8191>\
**Category:** User discussions\
**Tags:** mdrun, topology\
**Created:** [January 31, 2024, 11:58pm UTC](https://gromacs.bioexcel.eu/t/error-in-user-input-required-option-was-not-provided-and-the-default-file-topol-does-not-exist/8191 "2024-01-31T23:58:16Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![SoheilJamali](https://avatars.discourse-cdn.com/v4/letter/s/c37758/32.png) [@SoheilJamali](https://gromacs.bioexcel.eu/u/SoheilJamali)\
**Post date:** [January 31, 2024, 11:58pm UTC](https://gromacs.bioexcel.eu/t/error-in-user-input-required-option-was-not-provided-and-the-default-file-topol-does-not-exist/8191/1 "2024-01-31T23:58:16Z")

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I download my vesicle from the CHARMM-GUI website ([https://charmm-gui.org/](https://charmm-gui.org/)). I want to run it. I just run the README file which has commands for running. 6.0, 6.1 and 6.2 steps are running fine. but whenever I want to run step 6.3 on the supercomputer, it says the below error.

Program: gmx mdrun, version 2020.1

Error in user input:  
Invalid input values  
In option s  
Required option was not provided, and the default file ‘topol’ does not  
exist or is not accessible.  
The following extensions were tried to complete the file name:  
.tpr

Also, for running step 6.3, I have the step6.2\_equilibration.tpr.  
the commands that I use is this:  
gmx grompp -f step6.3\_equilibration.mdp -o step6.3\_equilibration.tpr -c step6.2\_equilibration.gro -p system.top -r lipidtail\_posres.pdb -n index.ndx

gmx mdrun -deffnm step6.3\_equilibration

what should I do?

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [February 1, 2024, 12:10am UTC](https://gromacs.bioexcel.eu/t/error-in-user-input-required-option-was-not-provided-and-the-default-file-topol-does-not-exist/8191/2 "2024-02-01T00:10:20Z")

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Check the error messages that `grompp` prints, because it failed to produce the `.tpr` file. Because it doesn’t exist, `mdrun` looks for a default file name, which it also doesn’t find, and then exits.

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**Author:** ![SoheilJamali](https://avatars.discourse-cdn.com/v4/letter/s/c37758/32.png) [@SoheilJamali](https://gromacs.bioexcel.eu/u/SoheilJamali)\
**Post date:** [February 1, 2024, 12:26am UTC](https://gromacs.bioexcel.eu/t/error-in-user-input-required-option-was-not-provided-and-the-default-file-topol-does-not-exist/8191/4 "2024-02-01T00:26:44Z")

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thanks for your answer. What should I do to solve this issue?

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [February 1, 2024, 3:39am UTC](https://gromacs.bioexcel.eu/t/error-in-user-input-required-option-was-not-provided-and-the-default-file-topol-does-not-exist/8191/5 "2024-02-01T03:39:51Z")

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> [@jalemkul](#):
>
> Check the error messages that `grompp` prints

^^ What I said before :)