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comparison tools/rdock/data/sf/RbtIonicAtoms.prm @ 3:b02d74d22d05 draft default tip

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author marpiech
date Mon, 29 Aug 2016 08:23:52 -0400
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2:bd50f811878f 3:b02d74d22d05
1 RBT_PARAMETER_FILE_V1.00
2 TITLE Receptor ionic atom definitions
3 VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtIonicAtoms.prm#2 $
4 ################################################################################
5 #
6 # Revision history:
7 #
8 # 21 Nov 2001 (DM) Added Heme Fe entries
9 # 19 Oct 2001 (DM) Extended list of metal ions
10 # 13 Jun 2000 (DM) Branched from RbtRNAScoringFunction.prm
11 # New format for ionic atoms (separate section for each residue)
12 #
13 ################################################################################
14 # Formal charges for RNA atoms
15 #
16 # A/ADE
17 #
18 SECTION A
19 O1P -0.5
20 O2P -0.5
21 END_SECTION
22
23 SECTION ADE
24 O1P -0.5
25 O2P -0.5
26 END_SECTION
27 #
28 # C/CYT
29 #
30 SECTION C
31 O1P -0.5
32 O2P -0.5
33 END_SECTION
34
35 SECTION CYT
36 O1P -0.5
37 O2P -0.5
38 END_SECTION
39 #
40 # G/GUA
41 #
42 SECTION G
43 O1P -0.5
44 O2P -0.5
45 END_SECTION
46
47 SECTION GUA
48 O1P -0.5
49 O2P -0.5
50 END_SECTION
51 #
52 # U/URA
53 #
54 SECTION U
55 O1P -0.5
56 O2P -0.5
57 END_SECTION
58
59 SECTION URA
60 O1P -0.5
61 O2P -0.5
62 END_SECTION
63
64 #################################################################################
65 # Formal charges for amino acids
66 #
67 # LYS+
68 #
69 SECTION LYS
70 HZ1 +0.333
71 HZ2 +0.333
72 HZ3 +0.333
73 END_SECTION
74 #
75 # ARG+
76 #
77 SECTION ARG
78 HE +0.167
79 HH11 +0.167
80 HH12 +0.167
81 HH21 +0.167
82 HH22 +0.167
83 CZ +0.167
84 END_SECTION
85 #
86 # HSP+
87 #
88 SECTION HSP
89 HD1 +0.333
90 HE2 +0.333
91 CE1 +0.333
92 END_SECTION
93
94 SECTION HIS
95 MANDATORY HD1,HE2
96 HD1 +0.333
97 HE2 +0.333
98 CE1 +0.333
99 END_SECTION
100 #
101 # ASP-
102 #
103 SECTION ASP
104 FORBIDDEN HD1,HD2
105 OD1 -0.5
106 OD2 -0.5
107 END_SECTION
108 #
109 # GLU-
110 #
111 SECTION GLU
112 FORBIDDEN HE1,HE2
113 OE1 -0.5
114 OE2 -0.5
115 END_SECTION
116
117 #################################################################################
118 # Formal charges for metal cations
119 #
120 SECTION NA
121 NA +1.0
122 END_SECTION
123
124 SECTION MG
125 MG +1.0
126 END_SECTION
127
128 SECTION K
129 K +1.0
130 END_SECTION
131
132 SECTION CA
133 CA +1.0
134 END_SECTION
135
136 SECTION V
137 V +1.0
138 END_SECTION
139
140 SECTION MN
141 MN +1.0
142 END_SECTION
143
144 SECTION FE
145 FE +1.0
146 END_SECTION
147
148 # Specific entries for GOLD PDB test set
149 SECTION FS4
150 FE1 +1.0
151 FE2 +1.0
152 FE3 +1.0
153 FE4 +1.0
154 END_SECTION
155
156 SECTION HEM
157 FE +1.0
158 END_SECTION
159
160 SECTION NI
161 NI +1.0
162 END_SECTION
163
164 SECTION ZN
165 ZN +1.0
166 END_SECTION
167
168 # Specific entries for ASTEX MOL2 test set
169 SECTION HG
170 HG +1.0
171 END_SECTION
172
173 SECTION CD
174 CD +1.0
175 END_SECTION
176
177 SECTION FS
178 FE1 +1.0
179 FE2 +1.0
180 FE3 +1.0
181 FE4 +1.0
182 END_SECTION
183
184 SECTION CO
185 CO +1.0
186 END_SECTION
187
188 #These metals occur in undefined residues
189 SECTION UNK
190 MG +1.0
191 MN +1.0
192 ZN +1.0
193 FE1 +1.0
194 FE2 +1.0
195 FE3 +1.0
196 FE4 +1.0
197 END_SECTION