ADL: keeping ligand in original conformation for first SAcycle

Rockey, William william-rockey at uiowa.edu
Tue Sep 28 12:45:30 PDT 2004


Hi,
 
I'm re-docking a ligand from a crystal structure to its receptor using SA, and I want the ligand to start the SA cycle in its original crystal structure orientation.
 
I'm using the following commands in the paramenter file:
 
move test.pdbq # small molecule file
about    -12.925 13.214 40.511 # small molecule center
 
# Initial Translation, Quaternion and Torsions
tran0  -12.925 13.214 40.511  # initial coordinates/A or "random"
quat0 1 0 0 0  # initial quaternion or "random"
ndihe 0  # number of initial torsions
torsdof 0 0.3113 # num. non-Hydrogen torsional DOF & coeff.
 
# Initial Translation, Quaternion and Torsion Step Sizes and Reduction Factors
tstep 0  # translation step/A
qstep 0  # quaternion step/deg
dstep 0  # torsion step/deg
trnrf 1.  # trans reduction factor/per cycle
quarf 1.  # quat reduction factor/per cycle
dihrf 1.  # tors reduction factor/per cycle
 
The xyz coordinates listed for the "about" parameter are the mean coordinates of the ligand.  The ligand came from the receptor used to make the grid maps, so the map coordinate set and the ligand coordinate set should be the same.  Therefore, I've set the "tran0" coordinates to the same values as the "about" coordinates.  My understanding is that one should be subtracted and the other added to the ligand coordinates, so in my case there should be no translation of the ligand.
 
But, the ligand orientation given under "Initial State" in my log file is quite different from my input ligand; it's both translated and rotated randomly each time I run AutoDock.  How can I keep the initial state of the ligand the same as it is in the crystal structure?
 
Thanks a lot for any help anyone can give!

Bill Rockey
University of Iowa
Dept. of Biochemistry




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