diff galaxy-tools/tools/rdock/data/sf/RbtInterIdxSF.prm @ 2:0faa03a92843 draft default tip

Uploaded

--- a/galaxy-tools/tools/rdock/data/sf/RbtInterIdxSF.prm	Fri Aug 26 09:55:15 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-RBT_PARAMETER_FILE_V1.00
-TITLE Intermolecular scoring function (without SOLVATION, indexed VDW)
-VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtInterIdxSF.prm#3 $
-
-################################################################################
-# Constant scoring function
-# Represents loss of translation, rotational entropy of ligand
-# DM 14 June 2006 - also calculates solvent penalty for all enabled solvent
-# SOLVENT_PENALTY is defined as a fraction of the ligand binding penalty
-# i.e. ligand binding penalty = 1.0 * WEIGHT
-# solvent binding penalty = N(enabled solvent) * SOLVENT_PENALTY * WEIGHT
-# 0.37 * 5.4 = 2.0 kJ/mol, which corresponds to GOLD Chemscore penalty
-# Verdonk et al, J. Med. Chem. 2005 (48) 6504-6515
-SECTION CONST
-	SCORING_FUNCTION	RbtConstSF
-	SOLVENT_PENALTY		0.37
-	WEIGHT			+5.4
-END_SECTION
-
-################################################################################
-# Rotational scoring function
-# Represents loss of torsional entropy of ligand
-SECTION ROT
-	SCORING_FUNCTION	RbtRotSF
-	WEIGHT			+1.0
-END_SECTION
-
-################################################################################
-# Pseudo SFs for setting up atomic attributes for polar and lipo atoms
-SECTION SETUP_POLAR
-	SCORING_FUNCTION	RbtSetupPolarSF
-	RADIUS			5.0
-	NORM			25
-	POWER			0.5
-	CHGFACTOR		0.5
-	GUANFACTOR		0.5
-END_SECTION
-
-################################################################################
-# Hydrogen-bond scoring function (also Metal-acceptor, C.cat - acceptor)
-SECTION POLAR
-	SCORING_FUNCTION	RbtPolarIdxSF
-	WEIGHT			3.4
-	R12FACTOR		1.0
-	R12INCR			0.05
-	DR12MIN		 	0.25
-	DR12MAX		 	0.6
-	A1			180.0
-	DA1MIN			30.0
-	DA1MAX			80.0
-	A2			180.0
-	DA2MIN			60.0
-	DA2MAX			100.0
-	INCMETAL		TRUE
-	INCHBD			TRUE
-	INCHBA			TRUE
-	INCGUAN			TRUE
-	GUAN_PLANE		TRUE
-	ABS_DR12		TRUE
-	GRIDSTEP		0.5
-	RANGE			5.31
-	INCR			3.36
-	ATTR			TRUE
-	LP_OSP2			TRUE
-	LP_PHI			45
-	LP_DPHIMIN		15
-	LP_DPHIMAX		30	
-	LP_DTHETAMIN		20
-	LP_DTHETAMAX		60
-END_SECTION
-
-################################################################################
-# Repulsive polar scoring function (donor-donor, acceptor-acceptor, metal-donor, C.cat-donor etc)
-SECTION REPUL
-	SCORING_FUNCTION	RbtPolarIdxSF
-	WEIGHT			5.0
-	R12FACTOR		1.0
-	R12INCR			0.6
-	DR12MIN			0.25
-	DR12MAX			1.1
-	A1			180.0
-	DA1MIN			30.0
-	DA1MAX			60.0
-	A2			180.0
-	DA2MIN			30.0
-	DA2MAX			60.0
-	INCMETAL		TRUE
-	INCHBD			TRUE
-	INCHBA			TRUE
-	INCGUAN			TRUE
-	GUAN_PLANE		FALSE
-	ABS_DR12		FALSE
-	GRIDSTEP		0.5
-	RANGE			5.32
-	INCR			3.51
-	ATTR			FALSE
-	LP_OSP2			FALSE
-END_SECTION
-
-################################################################################
-# Aromatic (pi-pi) scoring function, also used for cation-pi
-#SECTION AROM
-#	SCORING_FUNCTION	RbtAromIdxSF
-#	WEIGHT			-1.8
-#	R12 			3.5
-#	DR12MIN		 	0.25
-#	DR12MAX 		0.6
-#	DAMIN			20.0
-#	DAMAX			30.0
-#	GRIDSTEP		0.5
-#	RANGE			4.1
-#	INCR			4.1
-#END_SECTION
-
-################################################################################
-# Van der Waals scoring function
-SECTION VDW
-	SCORING_FUNCTION	RbtVdwIdxSF
-	WEIGHT			1.0
-	USE_4_8			FALSE
-	USE_TRIPOS		FALSE
-	RMAX			1.5
-	ECUT			120.0
-	E0			1.5
-	FAST_SOLVENT		TRUE
-END_SECTION