[gmx-users] fatal error: The solvent group non-Protein is not continuous

[Shima Arasteh]

Dear gmx users,

I am a new user of gromacs.


I solvated my protein in water. Now  I want to neutralize the system. I added 2 CL ions to the system but when run the following command, get the fatal error:

# genion -s ions.tpr -o monomer_solv_ions.gro -p topol.top -nname CL -nn 2

fatal error: The solvent group non-Protein is not continuous: index[2]=2, index[3]=237

I searched the mailing list and saw your suggestions about reordering the [ molecules ] section. But how is it? What does it mean? I did not get what to do.

Thanks in advance,
Shima
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