[Dock-fans] positive score in Amber

[Ben Keshet]

Hi Dock-fans,

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:
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? 
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?
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? 

Thank you for your help,
Ben