[gmx-users] Fatal error: 126 atoms are not part of any of the T-Coupling groups

[Joern Lenz]

dear users,
i am simulating a complex of DNA and protein.
also i looked through the mailing list I did not find any solution to my 
problem.

i am using make_ndx with:
 
make_ndx -f blah_ion -o blah_ion 

and in my mdp file i use:
 
tcoupl        = berendsen
tau_t         = 0.1       0.1  0.1  0.1  0.1  1.0   0.5   0.5   0.5   0.5         
tc_grps     = Protein   SOL  LYP  HIP  CYN  NA+   DG    DA    DC    DT    
ref_t         = 300       300  300  300  300  300   300   300   300   300        

make_ndx then asks me to choose of:

  0 System              : 317421 atoms
  1 Protein             :  6937 atoms
  2 Protein-H           :  3465 atoms
  3 C-alpha             :   445 atoms
  4 Backbone            :  1335 atoms
  5 MainChain           :  1780 atoms
  6 MainChain+Cb        :  2193 atoms
  7 MainChain+H         :  2205 atoms
  8 SideChain           :  4732 atoms
  9 SideChain-H         :  1685 atoms
 10 Prot-Masses         :  6937 atoms
 11 Non-Protein         : 310484 atoms
 12 LYP                 :   528 atoms
 13 HIP                 :   234 atoms
 14 CYN                 :    11 atoms
 15 DA                  :   192 atoms
 16 DG                  :   495 atoms
 17 DT                  :   192 atoms
 18 DC                  :   450 atoms
 19 SOL                 : 308340 atoms
 20 Na+                 :    42 atoms
 21 Other               : 310484 atoms

and i take the numbers: 1, 12, 13, 14, 15, 16, 17, 18, 19 and 20

I think I with this selection I have  no atom twice (otherwise there would be 
complaining of make_ndx) and covered all atoms in my system.
I looked through the top and pdb files and did not see any residues that are 
not mentiond in the table above.

=>> the same error occurs if i choose number 0 from the table above also -  
from my point of view this should cover all atoms at once, shouldn't it ?

Nevertheless I got the following error:
Fatal error:
126 atoms are not part of any of the T-Coupling groups

Do you have any suggestions or do I not see the wood for the trees any more ?
Thank you so much in advance