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How can I determine if a bond is rotatable in a ligand pdbq(t) file

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This FAQ applies to: AutoDock 3, AutoDock 4

The flexibility pattern for a ligand is encoded in its written pdbq(t) file by the inclusion of specific AutoDock keywords ROOT/ENDROOT, BRANCH/ENDBRANCH. However, it may not be simple to look at the file and determine which bonds are rotatable and which are not.
The overall flexibility pattern encoded in a ligand pdbq(t) file can visualized using ADT.
  • To do so:
  1. Read the previously-formatted-ligand molecule into ADT using File->Read Molecule
  2. Choose it to be ligand using Ligand->Choose
  3. You will then be given the choice of whether or not to  'Use Previous Torsion Tree'
=> choose Yes
    4.  You can then see which torsions are active using Ligand->Torsion Tree->Choose Torsions....

  • Another  way to determine whether a bond is treated as rotatable in ligand pdbq(t) file is to edit the file and look at the BRANCH statements, searching for the numbers of the two atoms in that specific bond.  Each BRANCH statement corresponds to one rotatable bond.  The  BRANCH statement includes the numbers of the corresponding atoms.  For example,  a bond between atoms numbered 12 and 27 is rotatable if the statement BRANCH 12 27 appears in the pdbq(t) file.

by Ruth Huey last modified 2007-08-01 11:31

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