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

Uploaded

--- a/galaxy-tools/tools/rdock/data/sf/RbtIonicAtoms.prm	Fri Aug 26 09:55:15 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,197 +0,0 @@
-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