# Erorr in energy minimization

**URL:** <https://gromacs.bioexcel.eu/t/erorr-in-energy-minimization/4352>\
**Category:** User discussions\
**Tags:** forcefield, grompp, mdrun, simulation-setup\
**Created:** [June 23, 2022, 11:23pm UTC](https://gromacs.bioexcel.eu/t/erorr-in-energy-minimization/4352 "2022-06-23T23:23:38Z")\
**Posts on this page:** 1\
**Showing post:** 4

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [June 25, 2022, 1:56am UTC](https://gromacs.bioexcel.eu/t/erorr-in-energy-minimization/4352/4 "2022-06-25T01:56:33Z")

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> [@weamalyoubi](#):
>
> NOTE 2 [file topol.top, line 102736]:  
> System has non-zero total charge: -76.469988  
> Total charge should normally be an integer. See  
> [Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic)  
> for discussion on how close it should be to an integer.

You still have the same underlying problem. You need to stop and fix the topology issue before trying to do anything. A fractional charge indicates a severe problem. Start by looking at your ligand.

> [@weamalyoubi](#):
>
> WARNING: Bad box in file solv\_ions.gro

You have a misformatted coordinate file.

> [@weamalyoubi](#):
>
> Warning: atom name 177205 in topol.top and solv\_ions.gro does not match (NA - OW)  
> Warning: atom name 177206 in topol.top and solv\_ions.gro does not match (NA - HW1)  
> Warning: atom name 177207 in topol.top and solv\_ions.gro does not match (NA - HW2)

Here, the problem is your coordinate file is out of order with respect to the topology. The contents of `[molecules]` must be in the same order as the coordinate file.

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