Atomtype CJ not found

User discussions
1

GROMACS version: 2020
GROMACS modification: No

Command line:
gmx grompp -f ions.mdp -c solv.gro -p gra.top -o ions.tpr

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 646744793
Generated 461266 of the 461280 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 461280 of the 461280 1-4 parameter combinations

ERROR 1 [file gra.top, line 34]:
Atomtype CJ not found

There was 1 note

Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1408)

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

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

What to do?
PS: Atom type is CJ in my Graphene topology file

2

CJ is not an atom type that is supported by any of the force fields that are natively in GROMACS. grompp is telling you that it can’t find it and therefore cannot assign LJ (or any other) parameters to it.

3

What can I do about it?
Do I need to edit the force field files?

4

How did you generate the topology? What tool or program wrote a CJ atom type?

5

Thank you for responding
I am following Andrea’s website for generating Carbon Nanotube topology
please take a look at it Modeling Carbon Nanotubes with GROMACS - Chembytes

6

The first steps of the tutorial walk you through creating a custom force field for this system. Follow those steps to build the system.