Gmx genion -s proteinions.tpr -o proteinions.gro -p protein.top -pname NA -nname CL -neutral

User discussions
1

gmx grompp -f em.mdp -c proteinions.gro -p protein.top -o proteinem.tpr

while using the following command I am getting the following error :-

ERROR 1 [file topol.top, line 58]:
No such moleculetype CL

2

The error says the molecule type in your system is not found in the topology you provided.

See here: https://www.researchgate.net/post/How-to-solve-ERROR-1-file-topoltop-line-183055-No-such-moleculetype-actinomycin-D-in-GROMACS

3

Thanks a lot for the guidance, I added CL to ions.itp file inside charmm and got the results…:)

4

Hi Snigdna,
you added ions with the command ‘Gmx genion’, right?
Perhaps you need to check the file ‘ions.itp’ under the folder of the force field you chose.
The ion name varies with the force field.
You need to keep it consistent.
For example, the name of Sodium Ion in OPLS-AA is ‘CL’, but it is ‘SOD’ in CHARMM36.
Hope it works for your case.

5

Yes, it worked…!..Thanks a lot…:)