Error: Atomtype N3 not found while trying to obtain ions.tpr

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GROMACS version: :-) GROMACS - gmx grompp, 2023.3-Homebrew (-:
GROMACS modification: No

Hello,
I have been trying to do MD simulation for a protein whose 3D structure is predicted by AlphaFold. The ligand is Aspartate molecule. I am following a similar approach to the Protein-Ligand GROMACS tutorial.

When I run this command gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr I get the following error.

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'ns_type'

NOTE 1 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to -101202217

ERROR 1 [file topol.top, line 35]:
  Atomtype N3 not found


There was 1 NOTE

-------------------------------------------------------
Program:     gmx grompp, version 2023.3-Homebrew
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1029)

Fatal error:
There was 1 error in input file(s)

I have included the forcefield parameters in mt topology file (topol.top)
I have not changed anything in my force field directory.

2

Most likely there’s a parameter/atom in your topology that involves the N3 type, but the type is not itself defined within [ atomtypes ] at the beginning of the topology (often included in forcefield.itp and then ffnonbonded.itp). You can check that by grepping within the relevant files.

This will depend on where you got your FF files from - most Amber FFs feature N3 for charged amino groups, so it’s easy to copy the entry from a compatible FF directory, but there might be a more complex reason why the atomtype was missing in the first place.

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