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

[Erik Marklund]

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.

/Erik

>> 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
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before  
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www  
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> ++++
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the www  
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_______________________________________________
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