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

Qiang Zhong zqiang320 at webmail.hzau.edu.cn
Wed Feb 7 14:34:44 CET 2007

      I have post my question last time,my emailbox can not work, So I post
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

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

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