GROMACS version: 2024.4
GROMACS modification: Yes
I tried to run a simulation for Protein-ligand Complex, in which ligand has a O+ atom on its structure. I faced an error during Energy Minimization that shows
Internal error (bug):
Step 0: The total potential energy is -nan, which is not finite. The LJ and
electrostatic contributions to the energy are nan and -672170, respectively. A
non-finite potential energy can be caused by overlapping interactions in
bonded interactions or very large or Nan coordinate values. Usually this is
caused by a badly- or non-equilibrated initial configuration, incorrect
interactions or parameters in the topology.
I did ligand parameterization using Swissparam and I used charmm36 force field. I literally stuck in this step for almost a month.
Could you guys help me to solve this?