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

[Qiang Zhong]

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:
grompp -n index.ndx -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o
fullmd.tpr

But Error still there.

Could somebody tell me how to do?
Thank you very much!




------------------------------
Qiang Zhong
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education 
College of Animal Sciences and Technology 
Huazhong Agricultural University
Wuhan,Hubei, 430070
PR China