Loading ...
Sorry, an error occurred while loading the content.
 

Refinement using RDC

Expand Messages
  • gamorim@cnrmn.bioqmed.ufrj.br
    Dear all, I m trying to refine a protein structure using RDC values (SANI). I included a pseudomolecule OXYZ (ANI) in mtf and pdb input files: MTF 1580
    Message 1 of 1 , Nov 23, 2005
      Dear all,

      I'm trying to refine a protein structure using RDC values (SANI). I
      included a pseudomolecule OXYZ (ANI) in mtf and pdb input files:

      MTF
      1580 ' ' '500' 'ANI' 'X' 'XXX' 0.000000E+00 10.0000
      1581 ' ' '500' 'ANI' 'Y' 'YYY' 0.000000E+00 10.0000
      1582 ' ' '500' 'ANI' 'Z' 'ZZZ' 0.000000E+00 10.0000
      1583 ' ' '500' 'ANI' 'OO' 'OOO' 0.000000E+00 10.0000

      bond connections
      1583 1580
      1583 1581
      1583 1582

      angle connections
      1580 1583 1581
      1580 1583 1582
      1581 1583 1582

      PDB
      ATOM 1580 X ANI 500 79.799 2.756 -1.165 1.00 3.06
      ATOM 1581 Y ANI 500 77.279 0.319 1.223 1.00 4.37
      ATOM 1582 Z ANI 500 81.248 1.138 2.478 1.00 4.35
      ATOM 1583 OO ANI 500 80.000 0.000 0.000 1.00 4.04


      During CNS calculation it returned the following error for all atoms:

      ....
      %atoms " -103 -ALA -N " and " -500 -ANI -X " only nan A apart
      %atoms " -103 -ALA -N " and " -500 -ANI -Y " only nan A apart
      %atoms " -103 -ALA -N " and " -500 -ANI -Z " only nan A apart
      %atoms " -103 -ALA -N " and " -500 -ANI -OO " only nan A apart
      %atoms " -103 -ALA -CA " and " -500 -ANI -X " only nan A apart
      %atoms " -103 -ALA -CA " and " -500 -ANI -Y " only nan A apart
      %atoms " -103 -ALA -CA " and " -500 -ANI -Z " only nan A apart
      %atoms " -103 -ALA -CA " and " -500 -ANI -OO " only nan A apart
      %atoms " -103 -ALA -CB " and " -500 -ANI -X " only nan A apart
      %atoms " -103 -ALA -CB " and " -500 -ANI -Y " only nan A apart
      %atoms " -103 -ALA -CB " and " -500 -ANI -Z " only nan A apart
      %atoms " -103 -ALA -CB " and " -500 -ANI -OO " only nan A apart
      NBONDS: found 8665 intra-atom interactions
      NBONDS: found 3152 nonbonded violations
      %SWEEPOUT2 error encountered: THERE IS A ZERO DETERMINANT
      (CNS is in mode: SET ABORT=NORMal END)
      *****************************************************
      ABORT mode will terminate program execution.
      *****************************************************
      Program will stop immediately.

      I'd appreciate any help.
      Thanks in advance,

      Gisele

      --
      Gisele Cardoso Amorim - Msc
      Centro Nacional de Ressonância Magnética Nuclear
      Instituto de Bioquímica Médica
      Universidade Federal do Rio de Janeiro
      Av. Brig. Trompowski, s/n.
      CCS - Bloco E - Sala 10
      Cidade Universitária - Ilha do Fundão
      Rio de Janeiro - Brasil

      Tel:55-21-25626756
      Fax:55-21-22708647
    Your message has been successfully submitted and would be delivered to recipients shortly.