<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div>Hi all,</div><div><br></div><div>After i ran grompp I've the following message:</div><div><br></div><div>Fatal error:</div><div>3 atoms are non part of any of the T-coupling groups</div><div><br></div><div>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</div><div><br></div><div>genion_d -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top</div><div><br></div><div>grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr</div><div><br></div><div>Additional information: I'm running GROMACS 4.5.5</div><div><br></div><div>Regards.<br></div></div></body></html>