# Lysozyme phosphate ion - coordinate issue

**URL:** <https://gromacs.bioexcel.eu/t/lysozyme-phosphate-ion-coordinate-issue/5231>\
**Category:** User discussions\
**Created:** [November 11, 2022, 9:19am UTC](https://gromacs.bioexcel.eu/t/lysozyme-phosphate-ion-coordinate-issue/5231 "2022-11-11T09:19:58Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![josh](https://avatars.discourse-cdn.com/v4/letter/j/45deac/32.png) [@josh](https://gromacs.bioexcel.eu/u/josh)\
**Post date:** [November 11, 2022, 9:19am UTC](https://gromacs.bioexcel.eu/t/lysozyme-phosphate-ion-coordinate-issue/5231/1 "2022-11-11T09:19:58Z")

</div>

Hi, I have tried replicating the lysozyme tutorial with one with phosphate ions, where parameters have been sourced and I have placed them within the charmm36.ff in the ions.itp.

(Where using: gmx genion -s ions.tpr -o 1AKI\_solv\_ions.gro -p topol.top -pname SOD -pq 1 -nname PO4 -nq -3 -conc 0.3 -neutral)

When I try to run the energy equilibration step ( gmx mdrun -v -deffnm em). The co-ordinates of the topology and the coordinate file do not match. Do I need to add other parameters in the files / how would I go about fixing this?

---

<div class="post-metadata">

**Author:** ![alexnas](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alexnas/32/1826_2.png) [@alexnas](https://gromacs.bioexcel.eu/u/alexnas)\
**Post date:** [November 14, 2022, 12:51pm UTC](https://gromacs.bioexcel.eu/t/lysozyme-phosphate-ion-coordinate-issue/5231/2 "2022-11-14T12:51:01Z")

</div>

The easiest answer is that you use the wrong routine. gmx genion is for single atoms only. The easiest way is ti use gmx insert-molecules for the PO4 first, then add water and replace required amount of water with Na+ ions afterwards.