[buster-discuss] how to solve ERROR: [run_buster-0043]

Nicolas Foos Nicolas.Foos at afmb.univ-mrs.fr
Mon May 21 15:08:45 CEST 2012

Dear Xavier,

I am not sure, but it seems that your problems come from the format of 
your Pdb file. Your error suggest that buster don't understand what  
your pdb file contain. Maybe it's a problem with the pdb version. Or it 
could be a problem with the restraint library used by Buster. Does your 
Pdb file contain nucleic acid? Have you try pdb2seq. Because you can 
have problem of connectivity or something wrong with the chain ID or 
residue number.



Le 21/05/12 14:08, xavier.kubiak at free.fr a écrit :
> Dear buster users,
> I am trying to final refine a protein structure usuing Buster 2.10 and have the following error occuring :
> ERROR : [run_buster-0043] an initial sanity check has
>           discovered some un-recoverable problems. These will
>           cause the program to stop: you should have a good
>           look at the detailed report to see what causes this
>           error ( ./01-BUSTER/Cycle-1/gelly_sanity_test.log ).
>           The TNT sequence file might give additional
>           information ( ./01-BUSTER/Cycle-1/TNT.seq ). You
>           could use other tools available for additional
>           checks ('pdbchk' to analyse the input PDB file,
>           'pdb2seq' when generating TNT sequence files
>           yourself or the various MakeTNT tools when
>           dealing/generating restraint dictionaries).
>     grep: ./01-BUSTER/Cycle-1/TNT.seq: No such file or directory
>     [: 840: -eq: unexpected operator
>     cat: ./01-BUSTER/Cycle-1/TNT.seq: input file is output file
>   ERROR : [refine-0057] problems in run_buster: see messages
>           above
> In the gelly_sanity_test.log file, part of the problems appears to come from the absence of COMBINE cards and NOTE BUSTER_COMBINE_RES cards in the TNT card input :
> ###There are no COMBINE cards to be found in the TNT card input
>   There are no NOTE BUSTER_COMBINE_RES cards to be found in the TNT card input###
> I already used this version on this computer to refine another protein structure without any kind of problems, but now when trying to refine this strucutre again (as I know it was working) the same error occurs suggesting it is not pdbfile-dependent.
> Another part of the problems might come from the  "WARNING:  Chain A    is of undefined type." comments for every chain present in the pdb file. But I also have this warning for the protein I already solved with buster which is quite surprising...
> I have run 'pdbchk' as sugegsted and no error occured.
> I have reinstalled the programm but it does not change anything.
> Any idea or comment would be of great help !
> Thanks
> Xavier
> Xavier Kubiak - PhD Student
> Unit of Adaptative and Functional Biology (CNRS EAC 4413)
> Paris Diderot University
> +33 1 57 27 83 69
> email : xavier.kubiak at free.fr
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