Cannot find position restraint file restraint.gro in CHARMM-GUI input files fro GROMACS

User discussions
1

GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No

Hi everyone! I’m a GROMACS newcomer. I actually testing the possibility of performing MD simulations on a protein at various pH levels using the CHARMM-GUI Solvent Builder, in order to generate the input files.
I am encountering the following error during the first step of energy minimization.

>gmx grompp -f energyminim.mdp -c ppo.gro -p topol.top -o em.tpr

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.

For better clarity, here attached the specific files.

topol.top (456 Bytes)
energyminim.mdp (525 Bytes)

Thanks in advance for any suggestion!

2

It should work (get past this error) by adding the -r option to gmx grompp: gmx grompp -f energyminim.mdp -c ppo.gro -r ppo.gro -p topol.top -o em.tpr. This means that you explicitly use ppo.gro as the target for restraints. This is almost always what you want to do during energy minimization. When you then proceed with equilibrations you will have to decide if you want to restrain to the original coordinates (ppo.gro) or to the output from the step before. Both can be valid in different situations.