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

[David van der Spoel]

Joern Lenz wrote:
> 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
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you probably should start by putting the file aminoacids.dat from Amber 
in your directory and make a new index file. then check the mailinglist 
for advise on how may charge groups you want to use.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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