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