Can I insert two ligands with almost same itp files?

User discussions
1

GROMACS version:2021
GROMACS modification: /No
Here post your question

I have two ligands, ligand1 is the acid form of a buffer with 0 charge, ligand2 is the basic form of a buffer with -1 charge. Two ligands are mostly identical except ligand2 does not have a hydrogen so it is -1 charged. I submit their PDB to acpype and got ligand1.gro/top/itp and ligand2.gro/top/itp files.

I use insert-molecules and update the topol.top files based on here. If only one ligand is inserted, there is no problem to run
gmx grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr -maxwarn 1

But if both ligands are inserted, the gmx grompp -f ions.mdp ... will give error:

Fatal error:
Syntax error - File ligand2.itp, line 3
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes

I have already put the itp lines in the very beginning of the topol.top file:

; Include forcefield parameters
#include "amber14sb.ff/forcefield.itp"
#include "ligand1.itp"
#include "ligand2.itp"
2

I got the solution, i.e. move (cut & paste) the [ atomtypes ] section from the ligand.itp to the topol.top under forcefield parameters

3

Can you please show how your topol.top looks after the modification?
I am also facing the same problem