Continuous Score - Revision history

Frodo at 18:46, 15 February 2014

2014-02-15T18:46:12Z

← Older revision		Revision as of 18:46, 15 February 2014
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	[[Category:~~DOCK6~~]]		[[Category:DOCK 6]]
	[[Category:DOCK:Scoring problem]]		[[Category:DOCK:Scoring problem]]

Therese: 2 revisions

2012-10-08T18:10:32Z

2 revisions

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Revision as of 18:10, 8 October 2012

JohnIrwin at 17:27, 27 September 2007

2007-09-27T17:27:31Z

← Older revision		Revision as of 17:27, 27 September 2007
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			Continuous scoring may be used to evaluate a ligand:receptor complex without the investment of a grid calculation, or to perform a more detailed calculation without the numerical approximation of the grid. When continuous scoring is requested, then score parameters normally supplied to grid, must also be supplied to DOCK. It is left to the user to make sure consistent values are supplied to both programs.

	~~Continuous scoring may~~ be ~~used to evaluate~~ a ~~ligand:receptor complex without~~ the ~~investment of a grid calculation~~, ~~or to perform a more detailed calculation without~~ the ~~numerical approximation~~ of the ~~grid. When continuous scoring~~ is ~~requested, then score parameters normally supplied to grid, must also be supplied to DOCK~~. It is ~~left to~~ the ~~user to make sure consistent values are supplied to both programs~~.		The distance dependence of the Lennard-Jones function is set with the cont_score_att_exp and cont_score_rep_exp parameters. Typically a 6-12 potential is used, but it can be softened up by using a 6-8 or 6-9 potential. Regardless of the exponent values selected, the same radii and well-depths are used. The distance dependence of the Coulombic function is set with the distance_dielectric parameter. The dielectric constant is adjusted with the cont_score_dielectric parameter.

	The distance dependence of the Lennard-Jones function is set with the cont_score_att_exp and cont_score_rep_exp parameters. Typically a 6-12 potential is used, but it can be softened up by using a 6-8 or 6-9 potential. Regardless of the exponent values selected, the same radii and well-depths are used. The distance dependence of the Coulombic function is set with the distance_dielectric parameter~~. The dielectric constant is adjusted with~~ the ~~cont_score_dielectric parameter.~~		NOTE: The following parameter definitions will use the format below:

	~~NOTE: The following parameter definitions will use the format below~~:		parameter_name [default] (value):
			#description

	~~parameter_name [default]~~ (~~value~~):		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.
	~~#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.~~		Continuous Score Parameters

	~~Continuous Score Parameters~~		* continuous_score_primary [no] (yes, no):

	* continuous_score_primary [no] (yes, no):
	#Flag to perform continuous non-grid based scoring as the primary		#Flag to perform continuous non-grid based scoring as the primary
	#scoring function		#scoring function
	* continuous_score_secondary [no] (yes, no):		* continuous_score_secondary [no] (yes, no):
	#Flag to perform continuous non-grid based scoring as the		#Flag to perform continuous non-grid based scoring as the
	#secondary scoring function		#secondary scoring function
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	cont_score_turn_off_es [yes] (yes, no):		cont_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


			[[Category:DOCK6]]
			[[Category:DOCK:Scoring problem]]

JohnIrwin at 22:53, 19 September 2006

2006-09-19T22:53:43Z

New page

Continuous scoring may be used to evaluate a ligand:receptor complex without the investment of a grid calculation, or to perform a more detailed calculation without the numerical approximation of the grid. When continuous scoring is requested, then score parameters normally supplied to grid, must also be supplied to DOCK. It is left to the user to make sure consistent values are supplied to both programs.

The distance dependence of the Lennard-Jones function is set with the cont_score_att_exp and cont_score_rep_exp parameters. Typically a 6-12 potential is used, but it can be softened up by using a 6-8 or 6-9 potential. Regardless of the exponent values selected, the same radii and well-depths are used. The distance dependence of the Coulombic function is set with the distance_dielectric parameter. The dielectric constant is adjusted with the cont_score_dielectric parameter.

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.

Continuous Score Parameters

* continuous_score_primary [no] (yes, no):
#Flag to perform continuous non-grid based scoring as the primary
#scoring function
* continuous_score_secondary [no] (yes, no):
#Flag to perform continuous non-grid based scoring as the
#secondary scoring function
o cont_score_rec_filename [receptor.mol2] (string):
#File that contains receptor coordinates
o cont_score_att_exp [6] (int):
#VDW Lennard-Jones potential attractive exponent
o cont_score_rep_ex [12] (int):
#VDW Lennard-Jones potential repulsive exponent
o cont_score_dielectric [4.0] (float):
#Dielectric constant for electrostatic term
o cont_score_vdw_scale [1] (float):
#Scalar multiplier of vdw energy component
+ (if cont_score_vdw_scale = 0)
cont_score_turn_off_vdw [yes] (yes, no):
#Flag to turn of vdw portion of scoring function
o cont_score_es_scale [1] (float):
#Scalar multiplier of electrostatic energy component
+ (if cont_score_es_scale = 0)
cont_score_turn_off_es [yes] (yes, no):
#Flag to turn of es portion of scoring function