Dear friends,

Currently, I am working with MD Simulation with GROMACS 2023 and everything has been going well. Except this one:

When I try the energy minimization with the below commands, such an error occurred

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

- gmx mdrun -v -deffnm em

I tried to increase the box size with the command:

- gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.4

But even when I set "-d 10.0", the problem still exists with other residues belong to the ligand so I believe there is a systematic problem with the ligand.

I used CGENFF to generate the "Ligand.str file". It works well in other cases (protein in complex with or without ligand". Also, I view the complex structure with Pymol and Discovery Studio 2021 but do not realize any abnormal sign of the complex, or it is because I do not know how to view correctly to identify errors.

So I am begging for your help, any help is appreciated.

Thank you and best regards.