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
[EMAIL PROTECTED]       [EMAIL PROTECTED]   http://folding.bmc.uu.se
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