# How to run a molecule which has O+ in it?

**URL:** https://gromacs.bioexcel.eu/t/how-to-run-a-molecule-which-has-o-in-it/11533
**Category:** User discussions
**Tags:** simulation-setup, energy-minization
**Created:** [February 12, 2025, 1:11pm UTC](https://gromacs.bioexcel.eu/t/how-to-run-a-molecule-which-has-o-in-it/11533 "2025-02-12T13:11:13Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![LoganathanK](https://avatars.discourse-cdn.com/v4/letter/l/f6c823/32.png) [@LoganathanK](https://gromacs.bioexcel.eu/u/LoganathanK)
#### Post date: [February 12, 2025, 1:11pm UTC](https://gromacs.bioexcel.eu/t/how-to-run-a-molecule-which-has-o-in-it/11533/1 "2025-02-12T13:11:13Z")

</div>

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?