[Dock-fans] regarding the DOCK6

Scott Brozell sbrozell at rci.rutgers.edu
Wed Nov 4 22:47:48 PST 2015


Hi,

The Amber score output in the Dock output contains energy terms for each
species (complex, receptor, and ligand) such that the sum of the terms is
equal to the score; in particular, note that the receptor and ligand values
have been negated.  Thus the AMBER score is calculated from the output as:
E(Complex) + -E(Receptor) + -E(Ligand)

See these for more details:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScoreEnergy
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScoreOutputs
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm

Assuming one considers the Amber score as a delta G then the
delta delta G is AmberScore - AmberScore.
This is a big assumption.  See these for more details:
http://mailman.docking.org/pipermail/dock-fans/2007-March/000973.html
http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#whatisascore

scott

On Wed, Nov 04, 2015 at 12:21:14PM +0530, Bindumadhuri Cavuturu wrote:
> I have a question regarding my dock6 analysis. In the dock.out file it was
> given the amberscore ,protein energy and the liand and for the complex as
> well. I have done it for the wild type and the mutant forms as well. now I
> want to calculate the DELTA DELTA G value but Iam confused to which value
> should I consider wheather AMBER score or the energy values for the complex
> ,receptor and the ligand. Kindly suggest me to rectify the doubt and to get
> clarified


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