GROMACS version:2024.1
GROMACS modification: No
Hi all,
I’m following the tutorial on Protein Ligand Complex by Dr. Lemkul and I encountered a problem with restraining the ligand. Protein-Ligand Complex
I followed the instructions and first restrained the H atoms on JZ4. Then I added restrain infomation at the end of topology file. I then grouped protein with ligand. Protein_JZ4 group appeared on my index.ndx file. So I procceeded with NVT equilibration steps, but this message showed up when I ran gmx mdrun -v -deffnm nvt: Update groups can not be used for this system because atoms that are (in)directly constrained together are interdispersed with other atoms. I tried to group multiple times but the message still showed up. Could anyone let me know what’s going on and how to fix it please? Thanks!
