annotate tools/rdock/data/sf/RbtIonicAtoms.prm @ 0:bc03dbb6eb37 draft

planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty

RBT_PARAMETER_FILE_V1.00
TITLE Receptor ionic atom definitions 
VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtIonicAtoms.prm#2 $
################################################################################
#
# Revision history:
#
# 21 Nov 2001 (DM) Added Heme Fe entries
# 19 Oct 2001 (DM) Extended list of metal ions
# 13 Jun 2000 (DM) Branched from RbtRNAScoringFunction.prm
#                  New format for ionic atoms (separate section for each residue)
#
################################################################################
# Formal charges for RNA atoms
#
# A/ADE
#
SECTION A
	O1P		-0.5
	O2P		-0.5
END_SECTION

SECTION ADE
	O1P		-0.5
	O2P		-0.5
END_SECTION
#
# C/CYT
#
SECTION C
	O1P		-0.5
	O2P		-0.5
END_SECTION

SECTION CYT
	O1P		-0.5
	O2P		-0.5
END_SECTION
#
# G/GUA
#
SECTION G
	O1P		-0.5
	O2P		-0.5
END_SECTION

SECTION GUA
	O1P		-0.5
	O2P		-0.5
END_SECTION
#
# U/URA
#
SECTION U
	O1P		-0.5
	O2P		-0.5
END_SECTION

SECTION URA
	O1P		-0.5
	O2P		-0.5
END_SECTION

#################################################################################
# Formal charges for amino acids
#
# LYS+
#
SECTION LYS
	HZ1		+0.333
	HZ2		+0.333
	HZ3		+0.333
END_SECTION
#
# ARG+
#
SECTION ARG
	HE		+0.167
	HH11		+0.167
	HH12		+0.167
	HH21		+0.167
	HH22		+0.167
	CZ		+0.167
END_SECTION
#
# HSP+
#
SECTION HSP
	HD1		+0.333
	HE2		+0.333
	CE1		+0.333
END_SECTION

SECTION HIS
	MANDATORY	HD1,HE2
	HD1             +0.333
        HE2             +0.333
        CE1             +0.333
END_SECTION
#
# ASP-
#
SECTION ASP
	FORBIDDEN	HD1,HD2
	OD1		-0.5
	OD2		-0.5
END_SECTION
#
# GLU-
#
SECTION GLU
	FORBIDDEN	HE1,HE2
	OE1		-0.5
	OE2		-0.5
END_SECTION

#################################################################################
# Formal charges for metal cations
#
SECTION NA
	NA		+1.0
END_SECTION

SECTION MG
	MG		+1.0
END_SECTION

SECTION K
	K		+1.0
END_SECTION

SECTION CA
	CA		+1.0
END_SECTION

SECTION V
	V		+1.0
END_SECTION

SECTION MN
	MN		+1.0
END_SECTION

SECTION FE
	FE		+1.0
END_SECTION

# Specific entries for GOLD PDB test set
SECTION FS4
	FE1		+1.0
	FE2		+1.0
	FE3		+1.0
	FE4		+1.0
END_SECTION

SECTION HEM
	FE		+1.0
END_SECTION

SECTION NI
	NI		+1.0
END_SECTION

SECTION ZN
	ZN		+1.0
END_SECTION

# Specific entries for ASTEX MOL2 test set
SECTION HG
	HG		+1.0
END_SECTION

SECTION CD
	CD		+1.0
END_SECTION

SECTION FS
	FE1		+1.0
	FE2		+1.0
	FE3		+1.0
	FE4		+1.0
END_SECTION

SECTION CO
	CO		+1.0
END_SECTION

#These metals occur in undefined residues
SECTION UNK
	MG		+1.0
	MN		+1.0
	ZN		+1.0
	FE1		+1.0
	FE2             +1.0
	FE3             +1.0
	FE4             +1.0
END_SECTION