[gmx-users] Fatal error: 126 atoms are not part of any of the T-Coupling groups
erikm at xray.bmc.uu.se
Wed Apr 18 11:54:10 CEST 2007
18 apr 2007 kl. 11.27 skrev 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
You should merge quite a few of the tc_groups, e.g. the DA/DC/DG/DT.
It doesn't solve the problem at hand, but can avoid problems further
down the road.
>> 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 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
> gmx-users mailing list gmx-users at gromacs.org
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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