[gmx-users] grompp error

Eduardo Oliveira eduardobio at yahoo.com.br
Tue Apr 3 20:51:01 CEST 2012

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

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