[gmx-users] Error:4 atoms are not part of any of the T-Coupling groups

[Mark Abraham]

Qiang Zhong wrote:
> Hollow:
>       I have post my question last time,my emailbox can not work, So I post
> again.
> I have 4 calcium ions bind at  protein, when I use command:
>  grompp  -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o fullmd.tpr
> 
> I got error message:
> Fatal error:
> 4 atoms are not part of any of the T-Coupling groups
> 
> I got a advice to use :
> make_ndx   -f  minimized_water.gro
> 
> Then I got a file index.ndx
> I find the line in index.ndx ,just like below:
> 57378 57379 57380 57381 
> [ CA ]
>    1    2    3    4 
> [ SOL ]
> Then I delete them,and run again:

That wasn't the advice Yang Ye gave you... see 
http://www.gromacs.org/pipermail/gmx-users/2007-February/025792.html

For a simpler solution, see 
http://www.gromacs.org/pipermail/gmx-users/2007-February/025796.html

Mark