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

xavier.kubiak at free.fr xavier.kubiak at free.fr
Mon May 21 14:08:21 CEST 2012

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

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 !

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

More information about the buster-discuss mailing list