ERROR No such moleculetype NA

GROMACS version:
GROMACS modification: Yes/No

I got this error
when I run the line: gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 10
in the topol.top there is 3 NA atoms

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GROMACS: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /mnt/d/Articles/Y MDs/Works/2022/Linani
Command line:
gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 0

Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’

NOTE 1 [file em.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 -2060518907
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117519 of the 167910 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_C’
Excluding 3 bonded neighbours molecule type ‘cp11’
Excluding 2 bonded neighbours molecule type ‘SOL’

ERROR 1 [file topol.top, line 109640]:
No such moleculetype NA

There was 1 note


Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2511)

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

Please how can I fix it?

Hi,
Such an error occurs when topol.top file do not include force-field-parameters information on a specific molecular type. In your case the problem is molecular type NA. Normally in force field ported to GROMACS, ions parameters are defined in ions.itp and this file needs to be included in the topology file.
Best regards
Alessandra

Hi Serta
Which forcefield are you using? In the latest charmm36-july2021 forcefield the sodium ions are represented by SOD and not NA. You can look into the ions.itp file in your forcefield directory and look for the correct naming. Once you locate the correct name you can update that in your .gro and topol.top files. I hope this helps. 😊