Hi all, After i ran grompp I've the following message:
Fatal error: 3 atoms are non part of any of the T-coupling groups It is probably in refference to the 3 CL atoms i've introduced into the system to neutralize my protein charge. Here are the command lines for genion and grompp genion_d -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr Additional information: I'm running GROMACS 4.5.5 Regards.
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