How to resolve failing Gromacs Membrane Protein Tutorial Energy Minimization step

User discussions
1

GROMACS version: 2021.4
GROMACS modification: No

I was trying Gromacs membrane protein tutorial.
I’ve reached Energy Minimization step.

But when I ran this code:

gmx grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr

I got this error:

Fatal error:
Cannot find position restraint file restraint.gro (option -r).
From GROMACS-2018, you need to specify the position restraint coordinate files
explicitly to avoid mistakes, although you can still use the same file as you
specify for the -c option.

Also with this:

gmx grompp -f minim.mdp -r system_solv_ions.gro -p topol.top -o em.tpr

I got the error:

Error in user input:
Invalid input values
  In option c
    Required option was not provided, and the default file 'conf' does not
    exist or is not accessible.
    The following extensions were tried to complete the file name:
      .gro, .g96, .pdb, .brk, .ent, .esp, .tpr

How can I resolve?

G.V.

2

You need to combine -c and -r:

gmx grompp -f minim.mdp -c system_solv_ions.gro -r system_solv_ions.gro -p topol.top -o em.tpr
1 Like
3

Thank you! This works.