Lysozyme phosphate ion - coordinate issue

User discussions
1

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?

2

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.