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

**URL:** <https://gromacs.bioexcel.eu/t/error-atomtype-n3-not-found-while-trying-to-obtain-ions-tpr/7726>\
**Category:** User discussions\
**Created:** [November 27, 2023, 12:33am UTC](https://gromacs.bioexcel.eu/t/error-atomtype-n3-not-found-while-trying-to-obtain-ions-tpr/7726 "2023-11-27T00:33:54Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![sam13](https://avatars.discourse-cdn.com/v4/letter/s/9de053/32.png) [@sam13](https://gromacs.bioexcel.eu/u/sam13)\
**Post date:** [November 27, 2023, 12:33am UTC](https://gromacs.bioexcel.eu/t/error-atomtype-n3-not-found-while-trying-to-obtain-ions-tpr/7726/1 "2023-11-27T00:33:54Z")

</div>

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.

```auto
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.

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<div class="post-metadata">

**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [November 27, 2023, 11:46am UTC](https://gromacs.bioexcel.eu/t/error-atomtype-n3-not-found-while-trying-to-obtain-ions-tpr/7726/2 "2023-11-27T11:46:47Z")

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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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<div class="post-metadata">

**Author:** ![FarzaneJP](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/farzanejp/32/1211_2.png) [@FarzaneJP](https://gromacs.bioexcel.eu/u/FarzaneJP)\
**Post date:** [November 27, 2023, 1:35pm UTC](https://gromacs.bioexcel.eu/t/error-atomtype-n3-not-found-while-trying-to-obtain-ions-tpr/7726/3 "2023-11-27T13:35:35Z")

</div>

These discussions may also help:

1. [Atomtype not found even though I #included the itp file](https://gromacs.bioexcel.eu/t/atomtype-not-found-even-though-i-included-the-itp-file/4241)

2. [Atomtype F not found](https://gromacs.bioexcel.eu/t/atomtype-f-not-found/1681)