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: | |||
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. | |||
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 | |||
[[Category:DOCK 6]] | |||
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):
- 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