Tutorial Protein-Ligand Complex error

User discussions
1

GROMACS version: 2022.1
GROMACS modification: No
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I am a new GROMACS user and I am trying to reproduce the protein-ligand complex tutorial. However, when I run the command “gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr” the following error appears:

“ERROR 1 [file topol.top, line 24633]:
No such moleculetype CL”

I did run “gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral” to add the ions and the end of the topology file was updated as illustrated in the tutorial:

“[ molecules ]
; Compound #mols
Protein_chain_A 1
JZ4 1
SOL 10229
CL 6”

How should I proceed to fix this issue?

Thank you!

2

If you’re using the July 2021 force field port instead of the March 2019 version that the tutorial calls for, the ions are now named exactly as they are in the CHARMM force field rather than adapting GROMACS conventions, so chloride ions are CLA, not CL.

3

Thank you so much! It is working perfectly now.