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view tools/rdock/data/sf/RbtPMFIdxSF.prm @ 5:a2f9c8a46a4b draft default tip

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planemo upload commit b9501ecca66b6a66c8cb87b945ad5f95181d7790-dirty
author marpiech
date Thu, 06 Oct 2016 07:09:26 -0400
parents 75f2b4087722
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RBT_PARAMETER_FILE_V1.00
TITLE Protein-ligand PMF (indexed version)
VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtPMFIdxSF.prm#2 $
################################################################################
#
# Revision history:
#
# References:
#
################################################################################
# Constant scoring function
# Represents loss of translation, rotational entropy of ligand
SECTION CONST
	SCORING_FUNCTION	RbtConstSF
	WEIGHT			+5.4	# Free-energy weighting
END_SECTION

################################################################################
# Rotational scoring function
# Represents loss of torsional entropy of ligand
SECTION ROT
	SCORING_FUNCTION	RbtRotSF
	WEIGHT			+1.0	# Free-energy weighting
END_SECTION

################################################################################
# Setup PMF atom types
SECTION SETUP_PMF
    	SCORING_FUNCTION    	RbtSetupPMFSF
END_SECTION

################################################################################
# Intermolecular PMF
SECTION PMF
        SCORING_FUNCTION        RbtPMFIdxSF
        SLOPE                   -3.0		# slope of the repulsive short-range linear term
        CC_CUTOFF                6.0		# count only shorter C_receptor - C_ligand interactions
        WEIGHT                   1.0
        GRIDSTEP                 1.0		# indexed grid distance (need not be dense) 
        BORDER                   1.0		#
        PMFDIR                   data/pmf	# ${RBT_ROOT/}data/pmf where the .pmfs are
END_SECTION
###############################################################################
#        OVERALL_CUTOFF           9.0		# value of overall cutoff (similar to C cutoff but for all types)