[Dock-fans] positive score in Amber

Scott Brozell sbrozell at scripps.edu
Thu Jul 26 12:51:30 PDT 2007


Hi,

On Thu, 26 Jul 2007, Ben Keshet wrote:

> I am using Amber score to dock the Grid score results.  However, I keep
> getting positive scores for all of my Amber runs and trying to understand
> why:

See my previous posts on errors in docking:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-July/001103.html

> 1. Does anyone know if the 4 steps of Amber (minimization, MD simulation,
> minimization, energy evaluation) are running once, or repeating until some
> parameter is reaching some value?

In general, see the fourth paragraph in this section of the manual:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
In particular, both minimizations will proceed until their maximum number
of cycles have been performed (amber_score_before_md_minimization_cycles
and amber_score_after_md_minimization_cycles), or until the root-mean-
square of the components of the gradient are less than 0.1.
(In Dock 6.2 0.1 will be an adjustable input parameter.)

> 2. What does the parameter amber_score_nonbonded_cutoff means? Does
> 'nonbonded' means non-bonded to the ligand or to the receptor? In other
> words, if my receptor is bigger than the amber_score_nonbonded_cutoff, some
> of it is not be included in the energy calculation?

In general, see that parameter description in this section of the manual:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
In particular, this cutoff is used to truncate the list of
nonbonded pairs (on an atom-by-atom basis) in every GB calculation.
See page 101 of the Amber 9 manual
http://amber.scripps.edu/doc9/index.html
Your second and third questions indicate that you do not understand the
basics of molecular dynamics.  Read section 1.1 of the Amber9 manual
for a description of useful texts.
The answer to the 2nd question is non-bonded over the set of all atoms.
The answer to the 3rd question is no in the sense that you probably mean.

> 3. Can anyone give me some hints on how to read the verbose OUT file to see
> whether I should increase the minimization steps or the MD steps?

In general, see the fourth last and the last paragraphs in this
section of the manual:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
In particular, for the minimizations plot the energy per step and
the rmsgrad per step.  Likewise for the MD
look for suspicious values and plot energy per step.

Amber score is not black box software.

Scott



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