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

[Yang Ye]

Interesting that you have your Ca2+ ions in the beginning of your 
structure file. In this case, remove the line [ SOL ] and replace [ CA ] 
with [ SOL ].
Although, changing your mdp file to have "Protein Non-Protein" is simpler.

The rationale behind is that the *groups* included for the tc-grps shall 
cover all atoms.

On 2/7/2007 9:34 PM, 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:
> 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
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