Minimization.gro does not exist

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1

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Hi guys,

I have downloaded files from Charmm Gui for a silica surface and these are shown below.

-README
-topol.top
-step5_production.mdp
-step4.1_equilibration.mdp
-step4.0 minimization.mdp
-step3_input.psf
-step3_input.pdb
-step3,input.gro

I need to run the following commands located in the README file and these are shown in bold (minimisation, equilibration and production). However, when I run the minimisation step, Ubuntu comes up with a error as I do not possess the minimization.gro file? Where do I get this file from?

Minimisation

gmx grompp -f step4.0_minimization.mdp -o step4.0_minimization.tpr -c step3_input.gro -r step3_input.gro -p topol.top -maxwarn 1
gmx_d mdrun -v -deffnm step4.0_minimization

Equilibration

gmx grompp -f step4.1_equilibration.mdp -o step4.1_equilibration.tpr -c step4.0_minimization.gro -r step3_input.gro -p topol.top
gmx mdrun -v -deffnm step4.1_equilibration

Production

gmx grompp -f step5_production.mdp -o step5_.tpr -cstep4.1_equilibration.gro -p topol.top
gmx mdrun -v -deffnm step5_

I would really appreciate any advice or help on this.

2

Hi Amo1997,

gmx grompp -f step4.0_minimization.mdp -o step4.0_minimization.tpr -c step3_input.gro -r step3_input.gro -p topol.top -maxwarn 1
gmx_d mdrun -v -deffnm step4.0_minimization

>>
You will have to edit the last minimization line from :
gmx_d mdrun -v -deffnm step4.0_minimization

to

gmx mdrun -v -deffnm step4.0_minimization

I think that should work.

Francis

3

Hi Francis,

I have tried that and I get the following message - 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.

I have the topol file in the directory but I do not know what the issue is. Do you have anymore suggestions?

Thank you.

4

So the error comes from mdrun? Please always copy and paste exact, full error messages. If the .tpr file doesn’t exist, then grompp failed and you need to investigate why that happened. There should be a clear fatal error and reason for it.

5

seems like you have not downloaded the topper folder, which has all related forcefields. If you check topology file you can see a path to topper folder and files