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

User discussions
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1

I download my vesicle from the CHARMM-GUI website (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?

2

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.

4

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

5

^^ What I said before :)