> > Hi Chitrita, may be you haven't generated index file for the solvent and newly added ions > use make_ndx file
> all the best Sudheer. > > 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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