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Refinement with anneal.inp

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  • jxqi2003
    Dear everyone: I first build up a model using ARP/wARP,delete the DUMP atoms, add the lost parts directly from the existing model(because of the sequence
    Message 1 of 1 , Feb 28, 2007
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      Dear everyone:

      I first build up a model using ARP/wARP,delete the "DUMP" atoms,
      add the lost parts directly from the existing model(because of the
      sequence identity) and then refine it with simulated annealing
      program(anneal.inp) in CNS.The error is:

      -------------------------- Torsion Topology -------------------------
      ----------
      ERROR: There are no suitable base groups.
      This problem can be caused by isolated
      bonding networks with undefined or weak
      dihedral force constants.
      The atoms that cannot be placed in a tree
      are listed below:
      %atoms " "-1 -LYS -CB
      %atoms " "-1 -LYS -CG
      %atoms " "-1 -LYS -CD
      %atoms " "-1 -LYS -CE
      %atoms " "-1 -LYS -NZ
      %atoms " "-1 -LYS -C
      %atoms " "-1 -LYS -O
      %atoms " "-1 -LYS -N
      %atoms " "-1 -LYS -CA
      %TORSION:TOPOLOGY error encountered: Fatal Topology Error
      (CNS is in mode: SET ABORT=NORMal END)

      I look at PDB file and find that the coordinates of these manually
      build parts are definitely seperated from those automatically build
      by the ARP/wARP program.

      Is there any hint? Any suggestion would be appreciated!

      Janxon
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