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

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 21 23:59:58 CEST 2012

On 4/21/12 1:17 PM, Shima Arasteh wrote:
> 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.

The error seems to indicate that you have some sort of broken molecule in your 
system.  What did you choose as the group into which ions were added?  If you 
chose "System" then ions may replace necessary components of the system.  The 
group to choose is whatever your solvent is.  Some basic tutorial material 
addresses such issues.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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