GROMACS version: 2021.4
GROMACS modification: no
Here post your question can anyone tell me how to solve this error i got after the gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr command.
I’m also getting
ERROR 15 [file fix.itp, line 40]:
Atomtype N5M not found
i created ligand Itp file using swissparam
Could you provide the contents of your topol.top file and the ligand itp file? The issue might be that the atoms were being called before they were actually defined.
Also, could you copy-paste the terminal output you got (warnings, error messages, notes) when you entered the command? And were there any errors/warnings/notes you got in any of the pervious steps or was this command the first step that received anything out of the ordinary?