Grid Based Score: Difference between revisions

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The grid-based score is based on the non-bonded terms of the molecular mechanic force field (see Grid for more background).


 
NOTE: The following parameter definitions will use the format below:
    The grid-based score is based on the non-bonded terms of the molecular mechanic force field (see Grid for more background).
 
    NOTE: The following parameter definitions will use the format below:


         parameter_name [default] (value):
         parameter_name [default] (value):
         #description
         #description


    In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.
In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.
 
Grid Score Parameters


    Grid Score Parameters
* grid_score_primary [yes] (yes, no):
# Flag to perform grid-based energy scoring as the primary scoring
#function
* grid_score_secondary [yes] (yes, no):
# Flag to perform grid-based energy scoring as the secondary #scoring function
* grid_score_vdw_scale [1] (float):
# Scalar multiplier of the VDW energy component
+ (if grid_score_vdw_scale = 0)
grid_score_turn_off_vdw [yes] (yes, no):
#Flag to turn of vdw portion of scoring function
* grid_score_es_scale [1] (float):
# The prefix to the grid files containing the desired energy
#grid
+ (if grid_score_es_scale = 0)
grid_score_turn_off_es [yes] (yes, no):
#Flag to turn of es portion of scoring function
* grid_score_grid_prefix [grid] (string):
#The prefix to the grid files containing the desired nrg grid


        * grid_score_primary [yes] (yes, no):
[[Category:DOCK 6]]
          # Flag to perform grid-based energy scoring as the primary scoring
          #function
        * grid_score_secondary [yes] (yes, no):
          # Flag to perform grid-based energy scoring as the secondary #scoring function
              o grid_score_vdw_scale [1] (float):
                # Scalar multiplier of the VDW energy component
                    + (if grid_score_vdw_scale = 0)
                      grid_score_turn_off_vdw [yes] (yes, no):
                      #Flag to turn of vdw portion of scoring function
              o grid_score_es_scale [1] (float):
                # The prefix to the grid files containing the desired energy
                #grid
                    + (if grid_score_es_scale = 0)
                      grid_score_turn_off_es [yes] (yes, no):
                      #Flag to turn of es portion of scoring function
              o grid_score_grid_prefix [grid] (string):
                #The prefix to the grid files containing the desired nrg grid

Latest revision as of 17:28, 15 February 2014

The grid-based score is based on the non-bonded terms of the molecular mechanic force field (see Grid for more background).

NOTE: The following parameter definitions will use the format below:

       parameter_name [default] (value):
       #description

In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.

Grid Score Parameters

  • grid_score_primary [yes] (yes, no):
  1. Flag to perform grid-based energy scoring as the primary scoring
  2. function
  • grid_score_secondary [yes] (yes, no):
  1. Flag to perform grid-based energy scoring as the secondary #scoring function
  • grid_score_vdw_scale [1] (float):
  1. Scalar multiplier of the VDW energy component

+ (if grid_score_vdw_scale = 0) grid_score_turn_off_vdw [yes] (yes, no):

  1. Flag to turn of vdw portion of scoring function
  • grid_score_es_scale [1] (float):
  1. The prefix to the grid files containing the desired energy
  2. grid

+ (if grid_score_es_scale = 0) grid_score_turn_off_es [yes] (yes, no):

  1. Flag to turn of es portion of scoring function
  • grid_score_grid_prefix [grid] (string):
  1. The prefix to the grid files containing the desired nrg grid