[gmx-users] Re:Error in T-coupling of 2 atoms in T-couplingGroups

sudheer babu sudheer.pbm07 at gmail.com
Thu Oct 2 12:00:08 CEST 2008

> Hi Chitrita,

may be you haven't generated index file for the solvent and newly added ions
use make_ndx file

> all the best

> I am a beginner of Gromacs 3.3.3.
> I have done position restrined grompp with -f pr.mdp, -r .gro (water box
> having charge -2e), -c .gro and -p .top (produced by genbox). The output is
> a .tpr file.
> Then to neutralize the solution with Na+ ion I used genion by -s .tpr -o
> .gro - pname NA+ -np 2 -g .log.
> Then in the .top file in [molecule] portion I have changed #mol of SOL by
> reducing it by 2 and added NA+ of 2 mol to match the coordinate with .gro.
> And also deleted the .tpr file. Upto this step everything was OK.
> In next step again position restrained grompp was done using .gro file
> containing 2 Na+ ions. But which showed a Fatal error --
> Fatal error:
> 2 atoms are not part of any of the T-coupling groups.
> So .tpr file is not generated. I am not understanding what to do now.....
> Please help as early as possible.
> Thanking you,
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