Subject: CCL:autodock3 parameter change

From: "Q." <qzou|at|iupui.edu>
Date: Fri, 19 Sep 2003 11:40:37 -0500

Subject: ADL: parameters
From: "Q." <qzou|at|iupui.edu>
To: autodock <autodock|at|scripps.edu>
Date: Fri, 19 Sep 2003 11:10:25 -0500

Dear All,
 I have a very hydrophobic ligand that only makes one h-bond to the
protein through a sp2 N atom.  There is a crystal structure the
protein/ligand complex. However, when I use autodock 3, the lowest
docked comformation is 3 anstrom away from the crystallofraphic
position. The 1 anstrom rmsd comformation has two fold less of delta G
than the experimental value.
 Buzko et. al. (2002) had once modified the parameters in autodock 2.4
to get the "right" docking position. They changed enthalpic well depth
for H-bond from 5 to 7.
 Now what is the justification to make such a change? If I want to
modify the 12-10 parameter or 12-6 parameter in autodock 3, although the
manual said not to change them lightly, how can I do it right?
 As a matter of factor, I have tried to increase to epsilonij for h-bond
to about 5~7, it did predict the right docking comformation with
reasonable binding free energy. However, these values are far away from
the one used in Autodock3, which is 0.328.
 Any suggestions are appreciated.

Qin Zou , Ph D.
Indiana University

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