Grid Based Score - Revision history

Frodo at 17:28, 15 February 2014

2014-02-15T17:28:53Z

← Older revision		Revision as of 17:28, 15 February 2014
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	* grid_score_grid_prefix [grid] (string):		* grid_score_grid_prefix [grid] (string):
	#The prefix to the grid files containing the desired nrg grid		#The prefix to the grid files containing the desired nrg grid

			[[Category:DOCK 6]]

Therese: 2 revisions

2012-10-08T20:25:24Z

2 revisions

← Older revision

Revision as of 20:25, 8 October 2012

Rgc: formatting

2011-09-26T22:18:33Z

formatting

← Older revision		Revision as of 22:18, 26 September 2011
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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):		* grid_score_primary [yes] (yes, no):
	# Flag to perform grid-based energy scoring as the primary scoring		# Flag to perform grid-based energy scoring as the primary scoring
	#function		#function
	* grid_score_secondary [yes] (yes, no):		* grid_score_secondary [yes] (yes, no):
	# Flag to perform grid-based energy scoring as the secondary #scoring function		# Flag to perform grid-based energy scoring as the secondary #scoring function
	o grid_score_vdw_scale [1] (float):		* grid_score_vdw_scale [1] (float):
	# Scalar multiplier of the VDW energy component		# Scalar multiplier of the VDW energy component
	+ (if grid_score_vdw_scale = 0)		+ (if grid_score_vdw_scale = 0)
	grid_score_turn_off_vdw [yes] (yes, no):		grid_score_turn_off_vdw [yes] (yes, no):
	#Flag to turn of vdw portion of scoring function		#Flag to turn of vdw portion of scoring function
	o grid_score_es_scale [1] (float):		* grid_score_es_scale [1] (float):
	# The prefix to the grid files containing the desired energy		# The prefix to the grid files containing the desired energy
	#grid		#grid
	+ (if grid_score_es_scale = 0)		+ (if grid_score_es_scale = 0)
	grid_score_turn_off_es [yes] (yes, no):		grid_score_turn_off_es [yes] (yes, no):
	#Flag to turn of es portion of scoring function		#Flag to turn of es portion of scoring function
	o grid_score_grid_prefix [grid] (string):		* grid_score_grid_prefix [grid] (string):
	#The prefix to the grid files containing the desired nrg grid		#The prefix to the grid files containing the desired nrg grid

JohnIrwin at 22:53, 19 September 2006

2006-09-19T22:53:07Z

New page

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
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