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amoebabio18.prm
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amoebabio18.prm
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##############################
## ##
## Force Field Definition ##
## ##
##############################
forcefield AMOEBA-BIO-2018
bond-cubic -2.55
bond-quartic 3.793125
angle-cubic -0.014
angle-quartic 0.000056
angle-pentic -0.0000007
angle-sextic 0.000000022
opbendtype ALLINGER
opbend-cubic -0.014
opbend-quartic 0.000056
opbend-pentic -0.0000007
opbend-sextic 0.000000022
torsionunit 0.5
vdwtype BUFFERED-14-7
radiusrule CUBIC-MEAN
radiustype R-MIN
radiussize DIAMETER
epsilonrule HHG
dielectric 1.0
polarization MUTUAL
vdw-12-scale 0.0
vdw-13-scale 0.0
vdw-14-scale 1.0
vdw-15-scale 1.0
mpole-12-scale 0.0
mpole-13-scale 0.0
mpole-14-scale 0.4
mpole-15-scale 0.8
polar-12-scale 0.0
polar-13-scale 0.0
polar-14-scale 1.0
polar-15-scale 1.0
polar-12-intra 0.0
polar-13-intra 0.0
polar-14-intra 0.5
polar-15-intra 1.0
direct-11-scale 0.0
direct-12-scale 1.0
direct-13-scale 1.0
direct-14-scale 1.0
mutual-11-scale 1.0
mutual-12-scale 1.0
mutual-13-scale 1.0
mutual-14-scale 1.0
#############################
## ##
## Literature References ##
## ##
#############################
This file contains the 2018 AMOEBA biopolymer force field, with contents
combined from the 2013 AMOEBA protein parameters and the 2017 AMOEBA nucleic
acid parameters as described in articles listed immediately below
Y. Shi, Z. Xia, J. Zhang, R. Best, J. W. Ponder and P. Ren, "Polarizable
Atomic Multipole-Based AMOEBA Force Field for Proteins", J. Chem. Theory
Comput., 9, 4046-4063 (2013)
C. Zhang, C. Lu, Z. Jing, C. Wu, J.-P. Piquemal, J. W. Ponder and P. Ren,
"AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids",
J. Chem. Theory Comput., 14, 2084-2108 (2018)
##################################################
## ##
## AMOEBA Biopolymer Force Field Atom Classes ##
## ##
## 1 Backbone Amide Nitrogen ##
## 2 Glycine Alpha Carbon ##
## 3 Backbone Carbonyl Carbon ##
## 4 Amide or Guanidinium Hydrogen ##
## 5 Amide Carbonyl Oxygen ##
## 6 Methine Hydrogen ##
## 7 Methine Carbon ##
## 8 Methyl or Methylene Carbon ##
## 9 Methyl or Methylene Hydrogen ##
## 10 Hydroxyl Oxygen ##
## 11 Hydroxyl Hydrogen ##
## 12 Sulfide or Disulfide Sulfur ##
## 13 Sulfhydryl Hydrogen ##
## 14 Thiolate Sulfur ##
## 15 Proline Backbone Nitrogen ##
## 16 Proline Ring Methylene Carbon ##
## 17 Phenyl Carbon ##
## 18 Phenyl Hydrogen ##
## 19 Phenolic Oxygen ##
## 20 Phenolic Hydrogen ##
## 21 Phenoxide Oxygen ##
## 22 Indole Carbon ##
## 23 Indole CH Hydrogen ##
## 24 Imidazole or Indole NH Nitrogen ##
## 25 Imidazole or Indole NH Hydrogen ##
## 26 Imidazole C=C Carbon ##
## 27 Imidazole CH Hydrogen ##
## 28 Imidazole N=C-N Carbon ##
## 29 Imidazole C=N Nitrogen ##
## 30 Carboxylate Carbon ##
## 31 Carboxylate Oxygen ##
## 32 Carboxylic Acid Carbonyl Oxygen ##
## 33 Carboxylic Acid Carbonyl Oxygen ##
## 34 Carboxylic Acid Hydroxyl Oxygen ##
## 35 Carboxylic Acid Hydrogen ##
## 36 Lysine/Ornithine Gamma Carbon ##
## 37 Ammonium Nitrogen ##
## 38 Ammonium Hydrogen ##
## 39 Guanidinium Carbon ##
## 40 Acetyl or NMe Methyl Carbon ##
## 41 N-Terminal Ammonium Nitrogen ##
## 42 N-Terminal Ammonium Hydrogen ##
## 43-64 Nucleotide Bases (ACGTU) ##
## 65-74 Ribose Sugar Ring ##
## 75-83 Deoxyribose Sugar Ring ##
## 84-89 DNA/RNA Terminal Groups ##
## ##
##################################################
#############################
## ##
## Atom Type Definitions ##
## ##
#############################
atom 1 1 N "Glycine N" 7 14.007 3
atom 2 2 CA "Glycine CA" 6 12.011 4
atom 3 3 C "Glycine C" 6 12.011 3
atom 4 4 HN "Glycine HN" 1 1.008 1
atom 5 5 O "Glycine O" 8 15.999 1
atom 6 6 H "Glycine HA" 1 1.008 1
atom 7 1 N "Alanine N" 7 14.007 3
atom 8 7 CA "Alanine CA" 6 12.011 4
atom 9 3 C "Alanine C" 6 12.011 3
atom 10 4 HN "Alanine HN" 1 1.008 1
atom 11 5 O "Alanine O" 8 15.999 1
atom 12 6 H "Alanine HA" 1 1.008 1
atom 13 8 C "Alanine CB" 6 12.011 4
atom 14 9 H "Alanine HB" 1 1.008 1
atom 15 7 C "Valine CB" 6 12.011 4
atom 16 6 H "Valine HB" 1 1.008 1
atom 17 8 C "Valine CG" 6 12.011 4
atom 18 9 H "Valine HG" 1 1.008 1
atom 19 8 C "Leucine CB" 6 12.011 4
atom 20 9 H "Leucine HB" 1 1.008 1
atom 21 7 C "Leucine CG" 6 12.011 4
atom 22 6 H "Leucine HG" 1 1.008 1
atom 23 8 C "Leucine CD" 6 12.011 4
atom 24 9 H "Leucine HD" 1 1.008 1
atom 25 7 C "Isoleucine CB" 6 12.011 4
atom 26 6 H "Isoleucine HB" 1 1.008 1
atom 27 8 C "Isoleucine CG1" 6 12.011 4
atom 28 9 H "Isoleucine HG1" 1 1.008 1
atom 29 8 C "Isoleucine CG2" 6 12.011 4
atom 30 9 H "Isoleucine HG2" 1 1.008 1
atom 31 8 C "Isoleucine CD" 6 12.011 4
atom 32 9 H "Isoleucine HD" 1 1.008 1
atom 33 8 C "Serine CB" 6 12.011 4
atom 34 9 H "Serine HB" 1 1.008 1
atom 35 10 OH "Serine OG" 8 15.999 2
atom 36 11 HO "Serine HG" 1 1.008 1
atom 37 7 C "Threonine CB" 6 12.011 4
atom 38 6 H "Threonine HB" 1 1.008 1
atom 39 10 OH "Threonine OG1" 8 15.999 2
atom 40 11 HO "Threonine HG1" 1 1.008 1
atom 41 8 C "Threonine CG2" 6 12.011 4
atom 42 9 H "Threonine HG2" 1 1.008 1
atom 43 8 C "Cysteine CB" 6 12.011 4
atom 44 9 H "Cysteine HB" 1 1.008 1
atom 45 12 SH "Cysteine SG" 16 32.066 2
atom 46 13 HS "Cysteine HG" 1 1.008 1
atom 47 12 SS "Cystine SG" 16 32.066 2
atom 48 7 CA "Cysteine Anion CA" 6 12.011 4
atom 49 14 S "Cysteine Anion S-" 16 32.066 1
atom 50 15 N "Proline N" 7 14.007 3
atom 51 7 CA "Proline CA" 6 12.011 4
atom 52 3 C "Proline C" 6 12.011 3
atom 53 5 O "Proline O" 8 15.999 1
atom 54 6 H "Proline HA" 1 1.008 1
atom 55 16 C "Proline CB" 6 12.011 4
atom 56 9 H "Proline HB" 1 1.008 1
atom 57 16 C "Proline CG" 6 12.011 4
atom 58 9 H "Proline HG" 1 1.008 1
atom 59 16 C "Proline CD" 6 12.011 4
atom 60 6 H "Proline HD" 1 1.008 1
atom 61 8 C "Phenylalanine CB" 6 12.011 4
atom 62 9 H "Phenylalanine HB" 1 1.008 1
atom 63 17 C "Phenylalanine CG" 6 12.011 3
atom 64 17 C "Phenylalanine CD" 6 12.011 3
atom 65 18 H "Phenylalanine HD" 1 1.008 1
atom 66 17 C "Phenylalanine CE" 6 12.011 3
atom 67 18 H "Phenylalanine HE" 1 1.008 1
atom 68 17 C "Phenylalanine CZ" 6 12.011 3
atom 69 18 H "Phenylalanine HZ" 1 1.008 1
atom 70 8 C "Tyrosine CB" 6 12.011 4
atom 71 9 H "Tyrosine HB" 1 1.008 1
atom 72 17 C "Tyrosine CG" 6 12.011 3
atom 73 17 C "Tyrosine CD" 6 12.011 3
atom 74 18 H "Tyrosine HD" 1 1.008 1
atom 75 17 C "Tyrosine CE" 6 12.011 3
atom 76 18 H "Tyrosine HE" 1 1.008 1
atom 77 17 C "Tyrosine CZ" 6 12.011 3
atom 78 19 OH "Tyrosine OH" 8 15.999 2
atom 79 20 HO "Tyrosine HH" 1 1.008 1
atom 80 8 C "Tyrosine Anion CB" 6 12.011 4
atom 81 9 H "Tyrosine Anion HB" 1 1.008 1
atom 82 17 C "Tyrosine Anion CG" 6 12.011 3
atom 83 17 C "Tyrosine Anion CD" 6 12.011 3
atom 84 18 H "Tyrosine Anion HD" 1 1.008 1
atom 85 17 C "Tyrosine Anion CE" 6 12.011 3
atom 86 18 H "Tyrosine Anion HE" 1 1.008 1
atom 87 17 C "Tyrosine Anion CZ" 6 12.011 3
atom 88 21 O- "Tyrosine Anion O-" 8 15.999 1
atom 89 8 C "Tryptophan CB" 6 12.011 4
atom 90 9 H "Tryptophan HB" 1 1.008 1
atom 91 22 C "Tryptophan CG" 6 12.011 3
atom 92 22 C "Tryptophan CD1" 6 12.011 3
atom 93 23 H "Tryptophan HD1" 1 1.008 1
atom 94 22 C "Tryptophan CD2" 6 12.011 3
atom 95 24 N "Tryptophan NE1" 7 14.007 3
atom 96 25 HN "Tryptophan HE1" 1 1.008 1
atom 97 22 C "Tryptophan CE2" 6 12.011 3
atom 98 22 C "Tryptophan CE3" 6 12.011 3
atom 99 23 H "Tryptophan HE3" 1 1.008 1
atom 100 22 C "Tryptophan CZ2" 6 12.011 3
atom 101 23 H "Tryptophan HZ2" 1 1.008 1
atom 102 22 C "Tryptophan CZ3" 6 12.011 3
atom 103 23 H "Tryptophan HZ3" 1 1.008 1
atom 104 22 C "Tryptophan CH2" 6 12.011 3
atom 105 23 H "Tryptophan HH2" 1 1.008 1
atom 106 8 C "Histidine (+) CB" 6 12.011 4
atom 107 9 H "Histidine (+) HB" 1 1.008 1
atom 108 26 C "Histidine (+) CG" 6 12.011 3
atom 109 24 N "Histidine (+) ND1" 7 14.007 3
atom 110 25 HN "Histidine (+) HD1" 1 1.008 1
atom 111 26 C "Histidine (+) CD2" 6 12.011 3
atom 112 27 H "Histidine (+) HD2" 1 1.008 1
atom 113 28 C "Histidine (+) CE1" 6 12.011 3
atom 114 27 H "Histidine (+) HE1" 1 1.008 1
atom 115 24 N "Histidine (+) NE2" 7 14.007 3
atom 116 25 HN "Histidine (+) HE2" 1 1.008 1
atom 117 8 C "Histidine (HD) CB" 6 12.011 4
atom 118 9 H "Histidine (HD) HB" 1 1.008 1
atom 119 26 C "Histidine (HD) CG" 6 12.011 3
atom 120 24 N "Histidine (HD) ND1" 7 14.007 3
atom 121 25 HN "Histidine (HD) HD1" 1 1.008 1
atom 122 26 C "Histidine (HD) CD2" 6 12.011 3
atom 123 27 H "Histidine (HD) HD2" 1 1.008 1
atom 124 28 C "Histidine (HD) CE1" 6 12.011 3
atom 125 27 H "Histidine (HD) HE1" 1 1.008 1
atom 126 29 N "Histidine (HD) NE2" 7 14.007 2
atom 127 8 C "Histidine (HE) CB" 6 12.011 4
atom 128 9 H "Histidine (HE) HB" 1 1.008 1
atom 129 26 C "Histidine (HE) CG" 6 12.011 3
atom 130 29 N "Histidine (HE) ND1" 7 14.007 2
atom 131 26 C "Histidine (HE) CD2" 6 12.011 3
atom 132 27 H "Histidine (HE) HD2" 1 1.008 1
atom 133 28 C "Histidine (HE) CE1" 6 12.011 3
atom 134 27 H "Histidine (HE) HE1" 1 1.008 1
atom 135 24 N "Histidine (HE) NE2" 7 14.007 3
atom 136 25 HN "Histidine (HE) HE2" 1 1.008 1
atom 137 8 C "Aspartate CB" 6 12.011 4
atom 138 9 H "Aspartate HB" 1 1.008 1
atom 139 30 C "Aspartate CG" 6 12.011 3
atom 140 31 O "Aspartate OD" 8 15.999 1
atom 141 8 C "Aspartic Acid CB" 6 12.011 4
atom 142 9 H "Aspartic Acid HB" 1 1.008 1
atom 143 32 C "Aspartic Acid CG" 6 12.011 3
atom 144 33 O "Aspartic Acid OD1" 8 15.999 1
atom 145 34 OH "Aspartic Acid OD2" 8 15.999 2
atom 146 35 HO "Aspartic Acid HD2" 1 1.008 1
atom 147 8 C "Asparagine CB" 6 12.011 4
atom 148 9 H "Asparagine HB" 1 1.008 1
atom 149 3 C "Asparagine CG" 6 12.011 3
atom 150 5 O "Asparagine OD1" 8 15.999 1
atom 151 1 N "Asparagine ND2" 7 14.007 3
atom 152 4 HN "Asparagine HD2" 1 1.008 1
atom 153 8 C "Glutamate CB" 6 12.011 4
atom 154 9 H "Glutamate HB" 1 1.008 1
atom 155 8 C "Glutamate CG" 6 12.011 4
atom 156 9 H "Glutamate HG" 1 1.008 1
atom 157 30 C "Glutamate CD" 6 12.011 3
atom 158 31 O "Glutamate OE" 8 15.999 1
atom 159 8 C "Glutamic Acid CB" 6 12.011 4
atom 160 9 H "Glutamic Acid HB" 1 1.008 1
atom 161 8 C "Glutamic Acid CG" 6 12.011 4
atom 162 9 H "Glutamic Acid HG" 1 1.008 1
atom 163 32 C "Glutamic Acid CD" 6 12.011 3
atom 164 33 O "Glutamic Acid OE1" 8 15.999 1
atom 165 34 O "Glutamic Acid OE2" 8 15.999 2
atom 166 35 H "Glutamic Acid HE2" 8 1.008 1
atom 167 8 C "Glutamine CB" 6 12.011 4
atom 168 9 H "Glutamine HB" 1 1.008 1
atom 169 8 C "Glutamine CG" 6 12.011 4
atom 170 9 H "Glutamine HG" 1 1.008 1
atom 171 3 C "Glutamine CD" 6 12.011 3
atom 172 5 O "Glutamine OE1" 8 15.999 1
atom 173 1 N "Glutamine NE2" 7 14.007 3
atom 174 4 HN "Glutamine HE2" 1 1.008 1
atom 175 8 C "Methionine CB" 6 12.011 4
atom 176 9 H "Methionine HB" 1 1.008 1
atom 177 8 C "Methionine CG" 6 12.011 4
atom 178 9 H "Methionine HG" 1 1.008 1
atom 179 12 S "Methionine SD" 16 32.066 2
atom 180 8 C "Methionine CE" 6 12.011 4
atom 181 9 H "Methionine HE" 1 1.008 1
atom 182 8 C "Lysine CB" 6 12.011 4
atom 183 9 H "Lysine HB" 1 1.008 1
atom 184 36 C "Lysine CG" 6 12.011 4
atom 185 9 H "Lysine HG" 1 1.008 1
atom 186 8 C "Lysine CD" 6 12.011 4
atom 187 9 H "Lysine HD" 1 1.008 1
atom 188 8 C "Lysine CE" 6 12.011 4
atom 189 9 H "Lysine HE" 1 1.008 1
atom 190 37 N "Lysine NZ" 7 14.007 4
atom 191 38 HN "Lysine HN" 1 1.008 1
atom 192 8 C "Lysine (Neutral) CB" 6 12.011 4
atom 193 9 H "Lysine (Neutral) HB" 1 1.008 1
atom 194 36 C "Lysine (Neutral) CG" 6 12.011 4
atom 195 9 H "Lysine (Neutral) HG" 1 1.008 1
atom 196 8 C "Lysine (Neutral) CD" 6 12.011 4
atom 197 9 H "Lysine (Neutral) HD" 1 1.008 1
atom 198 8 C "Lysine (Neutral) CE" 6 12.011 4
atom 199 9 H "Lysine (Neutral) HE" 1 1.008 1
atom 200 37 N "Lysine (Neutral) NZ" 7 14.007 3
atom 201 38 HN "Lysine (Neutral) HN" 1 1.008 1
atom 202 8 C "Arginine CB" 6 12.011 4
atom 203 9 H "Arginine HB" 1 1.008 1
atom 204 8 C "Arginine CG" 6 12.011 4
atom 205 9 H "Arginine HG" 1 1.008 1
atom 206 8 C "Arginine CD" 6 12.011 4
atom 207 9 H "Arginine HD" 1 1.008 1
atom 208 1 N "Arginine NE" 7 14.007 3
atom 209 4 HN "Arginine HE" 1 1.008 1
atom 210 39 C "Arginine CZ" 6 12.011 3
atom 211 1 N "Arginine NH" 7 14.007 3
atom 212 4 HN "Arginine HH" 1 1.008 1
atom 213 8 C "Ornithine CB" 6 12.011 4
atom 214 9 H "Ornithine HB" 1 1.008 1
atom 215 36 C "Ornithine CG" 6 12.011 4
atom 216 9 H "Ornithine HG" 1 1.008 1
atom 217 8 C "Ornithine CD" 6 12.011 4
atom 218 9 H "Ornithine HD" 1 1.008 1
atom 219 37 N "Ornithine NE" 7 14.007 4
atom 220 38 HN "Ornithine HE" 1 1.008 1
atom 221 40 C "Acetyl Cap CH3" 6 12.011 4
atom 222 6 H "Acetyl Cap H3C" 1 1.008 1
atom 223 3 C "Acetyl Cap C" 6 12.011 3
atom 224 5 O "Acetyl Cap O" 8 15.999 1
atom 225 1 N "Amide Cap NH2" 7 14.007 3
atom 226 4 HN "Amide Cap H2N" 1 1.008 1
atom 227 1 N "N-MeAmide Cap N" 7 14.007 3
atom 228 4 HN "N-MeAmide Cap HN" 1 1.008 1
atom 229 40 C "N-MeAmide Cap CH3" 6 12.011 4
atom 230 6 H "N-MeAmide Cap H3C" 1 1.008 1
atom 231 41 N "N-Terminal NH3+" 7 14.007 4
atom 232 42 H "N-Terminal H3N+" 1 1.008 1
atom 233 30 C "C-Terminal COO-" 6 12.011 3
atom 234 31 O "C-Terminal COO-" 8 15.999 1
atom 235 32 C "C-Terminal COOH C=O" 6 12.011 3
atom 236 33 O "C-Terminal COOH O=C" 8 15.999 1
atom 237 34 OH "C-Terminal COOH OH" 8 15.999 2
atom 238 35 HO "C-Terminal COOH HO" 1 1.008 1
atom 239 41 N "N-Terminal PRO NH2+" 7 14.007 4
atom 240 42 HN "N-Terminal PRO H2N+" 1 1.008 1
atom 241 7 CA "N-Terminal PRO CA" 6 12.011 4
atom 242 3 C "N-Terminal PRO C" 6 12.011 3
atom 243 5 O "N-Terminal PRO O" 8 15.999 1
atom 244 6 H "N-Terminal PRO HA" 1 1.008 1
atom 245 16 C "N-Terminal PRO CD" 6 12.011 4
atom 246 6 H "N-Terminal PRO HD" 1 1.008 1
atom 247 43 C "Adenine C4" 6 12.011 3
atom 248 44 C "Adenine C8" 6 12.011 3
atom 249 45 C "Adenine C6" 6 12.011 3
atom 250 43 C "Adenine C5" 6 12.011 3
atom 251 46 N "Adenine N9 RNA" 7 14.007 3
atom 252 46 N "Adenine N9 DNA" 7 14.007 3
atom 253 47 N "Adenine N6" 7 14.007 3
atom 254 48 C "Adenine C2" 6 12.011 3
atom 255 49 N "Adenine N7" 7 14.007 2
atom 256 50 N "Adenine N3" 7 14.007 2
atom 257 50 N "Adenine N1" 7 14.007 2
atom 258 51 H "Adenine H8" 1 1.008 1
atom 259 52 H "Adenine H2" 1 1.008 1
atom 260 53 H "Adenine H61" 1 1.008 1
atom 261 54 N "Cytosine N1 RNA" 7 14.007 3
atom 262 54 N "Cytosine N1 DNA" 7 14.007 3
atom 263 55 C "Cytosine C5" 6 12.011 3
atom 264 47 N "Cytosine N4" 7 14.007 3
atom 265 48 C "Cytosine C6" 6 12.011 3
atom 266 56 C "Cytosine C2" 6 12.011 3
atom 267 45 C "Cytosine C4" 6 12.011 3
atom 268 50 N "Cytosine N3" 7 14.007 2
atom 269 57 H "Cytosine H5" 1 1.008 1
atom 270 58 O "Cytosine O2" 8 15.999 1
atom 271 51 H "Cytosine H6" 1 1.008 1
atom 272 53 H "Cytosine H41" 1 1.008 1
atom 273 59 C "Guanine C2" 6 12.011 3
atom 274 56 C "Guanine C6" 6 12.011 3
atom 275 43 C "Guanine C4" 6 12.011 3
atom 276 44 C "Guanine C8" 6 12.011 3
atom 277 54 N "Guanine N1" 7 14.007 3
atom 278 47 N "Guanine N2" 7 14.007 3
atom 279 43 C "Guanine C5" 6 12.011 3
atom 280 60 N "Guanine N9 RNA" 7 14.007 3
atom 281 60 N "Guanine N9 DNA" 7 14.007 3
atom 282 49 N "Guanine N7" 7 14.007 2
atom 283 50 N "Guanine N3" 7 14.007 2
atom 284 61 H "Guanine H1" 1 1.008 1
atom 285 58 O "Guanine O6" 8 15.999 1
atom 286 51 H "Guanine H8" 1 1.008 1
atom 287 53 H "Guanine H21" 1 1.008 1
atom 288 62 C "Thymine C7" 6 12.011 4
atom 289 48 C "Thymine C5" 6 12.011 3
atom 290 56 C "Thymine C4" 6 12.011 3
atom 291 48 C "Thymine C6" 6 12.011 3
atom 292 63 N "Thymine N1" 7 14.007 3
atom 293 54 N "Thymine N3" 7 14.007 3
atom 294 56 C "Thymine C2" 6 12.011 3
atom 295 64 H "Thymine H7" 1 1.008 1
atom 296 58 O "Thymine O2" 8 15.999 1
atom 297 51 H "Thymine H6" 1 1.008 1
atom 298 58 O "Thymine O4" 8 15.999 1
atom 299 61 H "Thymine H3" 1 1.008 1
atom 300 56 C "Uracil C2" 6 12.011 3
atom 301 48 C "Uracil C6" 6 12.011 3
atom 302 56 C "Uracil C4" 6 12.011 3
atom 303 54 N "Uracil N3" 7 14.007 3
atom 304 63 N "Uracil N1" 7 14.007 3
atom 305 48 C "Uracil C5" 6 12.011 3
atom 306 61 H "Uracil H3" 1 1.008 1
atom 307 52 H "Uracil H5" 1 1.008 1
atom 308 58 O "Uracil O2" 8 15.999 1
atom 309 58 O "Uracil O4" 8 15.999 1
atom 310 51 H "Uracil H6" 1 1.008 1
atom 311 65 O "Ribose O4'" 8 15.999 2
atom 312 66 C "Ribose C4'" 6 12.011 4
atom 313 67 H "Ribose H4'" 1 1.008 1
atom 314 68 C "Ribose C1'" 6 12.011 4
atom 315 67 H "Ribose H1'" 1 1.008 1
atom 316 68 C "Ribose C2'" 6 12.011 4
atom 317 67 H "Ribose H2'1" 1 1.008 1
atom 318 68 C "Ribose C3'" 6 12.011 4
atom 319 67 H "Ribose H3'" 1 1.008 1
atom 320 69 O "Ribose O2'" 8 15.999 2
atom 321 70 H "Ribose HO'2" 1 1.008 1
atom 322 71 O "Ribose O3'" 8 15.999 2
atom 323 70 H "Ribose HO'3" 1 1.008 1
atom 324 72 C "Ribose C5'" 6 12.011 4
atom 325 73 H "Ribose H5'" 1 1.008 1
atom 326 74 O "Ribose O5'" 8 15.999 2
atom 327 70 H "Ribose HO'5" 1 1.008 1
atom 328 75 C "Deoxyribose C4'" 6 12.011 4
atom 329 76 C "Deoxyribose C3'" 6 12.011 4
atom 330 76 C "Deoxyribose C2'" 6 12.011 4
atom 331 76 C "Deoxyribose C1'" 6 12.011 4
atom 332 77 O "Deoxyribose O4'" 8 15.999 2
atom 333 78 H "Deoxyribose H2'1" 1 1.008 1
atom 334 78 H "Deoxyribose H1'" 1 1.008 1
atom 335 78 H "Deoxyribose H3'" 1 1.008 1
atom 336 78 H "Deoxyribose H4'" 1 1.008 1
atom 337 79 C "Deoxyribose C5'" 6 12.011 4
atom 338 80 O "Deoxyribose O3'" 8 15.999 2
atom 339 81 H "Deoxyribose HO'3" 1 1.008 1
atom 340 82 H "Deoxyribose H5'1" 1 1.008 1
atom 341 83 O "Deoxyribose O5'" 8 15.999 2
atom 342 81 H "Deoxyribose HO'5" 1 1.008 1
atom 343 84 P "Phosphodiester P" 15 30.974 4
atom 344 85 O "Phosphodiester OP" 8 15.999 1
atom 345 86 O "R-5'-Hydroxyl O5'T" 8 15.999 2
atom 346 87 O "R-3'-Hydroxyl O3'T" 8 15.999 2
atom 347 88 O "D-3'-Hydroxyl O3'T" 8 15.999 2
atom 348 89 O "D-5'-Hydroxyl O5'T" 8 15.999 2
atom 349 90 O "AMOEBA Water O" 8 15.999 2
atom 350 91 H "AMOEBA Water H" 1 1.008 1
atom 351 92 Li+ "Lithium Ion Li+" 3 6.941 0
atom 352 93 Na+ "Sodium Ion Na+" 11 22.990 0
atom 353 94 K+ "Potassium Ion K+" 19 39.098 0
atom 354 95 Rb+ "Rubidium Ion Rb+" 37 85.468 0
atom 355 96 Cs+ "Cesium Ion Cs+" 55 132.905 0
atom 356 97 Be+ "Beryllium Ion Be+2" 4 9.012 0
atom 357 98 Mg+ "Magnesium Ion Mg+2" 12 24.305 0
atom 358 99 Ca+ "Calcium Ion Ca+2" 20 40.078 0
atom 359 100 Zn+ "Zinc Ion Zn+2" 30 65.380 0
atom 360 101 F- "Fluoride Ion F-" 9 18.998 0
atom 361 102 Cl- "Chloride Ion Cl-" 17 35.453 0
atom 362 103 Br- "Bromide Ion Br-" 35 79.904 0
atom 363 104 I- "Iodide Ion I-" 53 126.904 0
atom 400 400 Fe2 "Ferric Ion Fe2+" 26 55.85 0
atom 401 401 Fe3 "Ferrous Ion Fe3+" 26 55.85 0
atom 501 37 N "gdma " 7 14.007 4
atom 502 8 C "gdma " 6 12.011 4
atom 503 8 C "gdma " 6 12.011 4
atom 504 9 H "gdma " 1 1.008 1
atom 505 37 N "gdma " 7 14.007 4
atom 506 9 H "gdma " 1 1.008 1
atom 507 8 C "gdma " 6 12.011 4
atom 508 8 C "gdma " 6 12.011 4
atom 509 9 H "gdma " 1 1.008 1
atom 510 37 N "gdma " 7 14.007 4
atom 511 9 H "gdma " 1 1.008 1
atom 512 8 C "gdma " 6 12.011 4
atom 513 8 C "gdma " 6 12.011 4
atom 514 9 H "gdma " 1 1.008 1
atom 515 37 N "gdma " 7 14.007 4
atom 516 9 H "gdma " 1 1.008 1
atom 517 8 C "gdma " 6 12.011 4
atom 518 8 C "gdma " 6 12.011 4
atom 519 9 H "gdma " 1 1.008 1
atom 520 37 N "gdma " 7 14.007 4
atom 521 9 H "gdma " 1 1.008 1
atom 522 8 C "gdma " 6 12.011 4
atom 523 9 H "gdma " 1 1.008 1
atom 524 38 H "gdma " 1 1.008 1
atom 525 38 H "gdma " 1 1.008 1
atom 526 38 H "gdma " 1 1.008 1
atom 527 38 H "gdma " 1 1.008 1
atom 528 8 C "gdma " 6 12.011 4
atom 529 9 H "gdma " 1 1.008 1
atom 530 38 H "gdma " 1 1.008 1
################################
## ##
## Van der Waals Parameters ##
## ##
################################
vdw 1 3.7100 0.1100
vdw 2 3.8200 0.1010
vdw 3 3.8200 0.1060
vdw 4 2.5900 0.0220 0.900
vdw 5 3.3000 0.1120
vdw 6 2.9400 0.0260 0.910
vdw 7 3.6500 0.1010
vdw 8 3.8200 0.1010
vdw 9 2.9800 0.0240 0.920
vdw 10 3.4050 0.1100
vdw 11 2.6550 0.0135 0.910
vdw 12 4.0050 0.3550
vdw 14 4.2000 0.3550
vdw 13 3.0000 0.0265 0.980
vdw 15 3.7100 0.1100
vdw 16 3.8200 0.1010
vdw 17 3.8000 0.0890
vdw 18 2.9800 0.0260 0.920
vdw 19 3.4050 0.1100
vdw 20 2.6550 0.0135 0.910
vdw 21 3.3200 0.1120
vdw 22 3.8000 0.1010
vdw 23 2.9800 0.0260 0.920
vdw 24 3.7100 0.1100
vdw 25 2.5900 0.0220 0.900
vdw 26 3.8000 0.1010
vdw 27 2.9800 0.0260 0.920
vdw 28 3.8000 0.1010
vdw 29 3.7100 0.1100
vdw 30 3.8200 0.1060
vdw 31 3.5500 0.0950
vdw 32 3.8200 0.1060
vdw 33 3.3000 0.1120
vdw 34 3.4050 0.1100
vdw 35 2.6550 0.0150 0.910
vdw 36 3.8200 0.1010
vdw 37 3.8100 0.1050
vdw 38 2.4800 0.0130 0.910
vdw 39 3.6500 0.1010
vdw 40 3.8200 0.1010
vdw 41 3.7600 0.1050
vdw 42 2.7000 0.0200 0.910
vdw 43 3.7200 0.1120
vdw 44 3.7400 0.1060
vdw 45 3.7200 0.1060
vdw 46 3.7000 0.1270
vdw 47 3.6000 0.1240
vdw 48 3.7400 0.1060
vdw 49 3.6400 0.1270
vdw 50 3.6400 0.1270
vdw 51 2.9500 0.0290 0.920
vdw 52 3.0800 0.0290 0.920
vdw 53 2.6500 0.0200 0.880
vdw 54 3.7000 0.1270
vdw 55 3.7900 0.1060
vdw 56 3.7200 0.0950
vdw 57 3.0500 0.0290 0.910
vdw 58 3.3500 0.1290
vdw 59 3.7200 0.1060
vdw 60 3.7000 0.1270
vdw 61 2.6500 0.0200 0.890
vdw 62 3.8000 0.1010
vdw 63 3.7000 0.1270
vdw 64 2.9000 0.0250 0.910
vdw 65 3.4050 0.1120
vdw 66 3.8200 0.1010
vdw 67 2.8900 0.0240 0.920
vdw 68 3.8200 0.1010
vdw 69 3.4050 0.1120
vdw 70 2.6550 0.0135 0.910
vdw 71 3.4500 0.1080
vdw 72 3.8200 0.1010
vdw 73 2.9400 0.0240 0.920
vdw 74 3.4500 0.1080
vdw 75 3.8200 0.1010
vdw 76 3.8200 0.1010
vdw 77 3.4050 0.1120
vdw 78 2.8900 0.0240 0.920
vdw 79 3.8200 0.1010
vdw 80 3.4500 0.1080
vdw 81 2.6550 0.0135 0.910
vdw 82 2.9400 0.0240 0.920
vdw 83 3.4500 0.1080
vdw 84 4.4500 0.3000
vdw 85 3.4000 0.1100
vdw 86 3.4050 0.1120
vdw 87 3.4050 0.1120
vdw 88 3.4050 0.1120
vdw 89 3.4050 0.1120
vdw 90 3.4050 0.1100
vdw 91 2.6550 0.0135 0.910
vdw 92 2.2000 0.0660
vdw 93 2.9550 0.2800
vdw 94 3.6800 0.3500
vdw 95 3.9000 0.3800
vdw 96 4.1400 0.4200
vdw 97 1.8800 0.0910
vdw 98 2.9000 0.2800
vdw 99 3.5900 0.3500
vdw 100 2.6800 0.2220
vdw 101 3.4300 0.2500
vdw 102 4.1200 0.3400
vdw 103 4.3200 0.4300
vdw 104 4.6100 0.5200
vdw 400 2.0550 0.1870
vdw 401 2.0500 0.2710
#####################################
## ##
## Van der Waals Pair Parameters ##
## ##
#####################################
vdwpr 4 31 3.1000 0.0400
vdwpr 5 98 3.0000 0.1530
vdwpr 5 99 3.2700 0.1750
vdwpr 5 100 2.8900 0.1750
vdwpr 49 93 3.3870 0.2400
vdwpr 49 94 3.6760 0.2900
vdwpr 49 98 3.4250 0.2150
vdwpr 50 93 3.3870 0.2400
vdwpr 50 94 3.6760 0.2900
vdwpr 50 98 3.4250 0.2150
vdwpr 58 98 3.2130 0.1820
vdwpr 94 102 4.2360 0.1512
vdwpr 94 103 4.3790 0.1664
vdwpr 94 104 4.6360 0.1720
vdwpr 95 102 4.3150 0.1859
vdwpr 95 103 4.4480 0.2068
vdwpr 95 104 4.6900 0.2145
vdwpr 96 102 4.3450 0.2894
vdwpr 96 103 4.4750 0.3307
vdwpr 96 104 4.7110 0.3466
##################################
## ##
## Bond Stretching Parameters ##
## ##
##################################
bond 1 2 375.00 1.4370
bond 1 3 482.00 1.3450
bond 1 4 487.00 1.0280
bond 1 7 375.00 1.4370
bond 1 8 374.80 1.4460
bond 1 39 491.40 1.3250
bond 1 40 375.00 1.4370
bond 2 3 345.00 1.5090
bond 2 6 341.00 1.1120
bond 2 30 345.00 1.5090
bond 2 32 345.00 1.5090
bond 2 41 381.30 1.4480
bond 3 5 662.00 1.2255
bond 3 7 345.00 1.5090
bond 3 8 345.00 1.5090
bond 3 15 482.00 1.3450
bond 3 40 345.00 1.5090
bond 6 7 341.00 1.1120
bond 6 16 341.00 1.1120
bond 6 40 341.00 1.1120
bond 7 7 323.00 1.5250
bond 7 8 323.00 1.5250
bond 7 10 410.00 1.4130
bond 7 15 375.00 1.4370
bond 7 16 323.00 1.5250
bond 7 30 345.00 1.5090
bond 7 32 345.00 1.5090
bond 7 41 381.30 1.4480
bond 8 8 323.00 1.5250
bond 8 9 341.00 1.1120
bond 8 10 410.00 1.4130
bond 8 12 215.80 1.8050
bond 8 14 215.80 1.8130
bond 8 17 453.20 1.4990
bond 8 22 345.00 1.5090
bond 8 26 453.20 1.4930
bond 8 30 345.00 1.5090
bond 8 32 345.00 1.5090
bond 8 36 323.00 1.5250
bond 8 37 381.30 1.4480
bond 9 16 341.00 1.1120
bond 9 36 341.00 1.1120
bond 10 11 548.90 0.9470
bond 12 12 188.50 2.0190
bond 12 13 278.40 1.3420
bond 15 16 375.00 1.4370
bond 16 16 323.00 1.5247
bond 16 41 381.30 1.4480
bond 17 17 471.90 1.3887
bond 17 18 370.50 1.1000
bond 17 19 431.60 1.3550
bond 17 21 680.00 1.2747
bond 19 20 548.90 0.9470
bond 22 22 471.90 1.3887
bond 22 23 370.50 1.1010
bond 22 24 653.90 1.3550
bond 24 25 467.60 1.0300
bond 24 26 653.90 1.3730
bond 24 28 653.90 1.3520
bond 26 26 539.60 1.3710
bond 26 27 370.50 1.0810
bond 26 29 670.00 1.3740
bond 27 28 370.50 1.0810
bond 28 29 670.00 1.3270
bond 30 31 705.00 1.2553
bond 32 33 705.00 1.2255
bond 32 34 431.60 1.3498
bond 34 35 514.40 0.9737
bond 37 38 461.90 1.0150
bond 41 42 461.90 1.0150
bond 43 43 268.00 1.4040
bond 43 45 340.00 1.4060
bond 43 46 340.00 1.3700
bond 43 49 460.00 1.3720
bond 43 50 340.00 1.3500
bond 43 56 340.00 1.4370
bond 43 60 340.00 1.3700
bond 44 46 400.00 1.3620
bond 44 49 478.00 1.3350
bond 44 51 420.00 1.0760
bond 44 60 400.00 1.3620
bond 45 47 420.00 1.3550
bond 45 50 400.00 1.3260
bond 45 55 390.00 1.4200
bond 46 68 390.00 1.4320
bond 46 76 390.00 1.4320
bond 47 53 540.00 1.0040
bond 47 59 420.00 1.3610
bond 48 48 420.00 1.3530
bond 48 50 400.00 1.3340
bond 48 51 405.00 1.0810
bond 48 52 405.00 1.0810
bond 48 54 400.00 1.3420
bond 48 55 390.00 1.3810
bond 48 56 420.00 1.4450
bond 48 62 360.00 1.4930
bond 48 63 400.00 1.3420
bond 50 56 478.00 1.3690
bond 50 59 400.00 1.3100
bond 54 56 325.00 1.3970
bond 54 59 400.00 1.3660
bond 54 61 512.00 1.0110
bond 54 68 360.00 1.4150
bond 54 76 360.00 1.4150
bond 55 57 408.00 1.0800
bond 56 58 530.00 1.2240
bond 56 63 325.00 1.3970
bond 60 68 390.00 1.4320
bond 60 76 390.00 1.4320
bond 61 63 512.00 1.0110
bond 62 64 384.00 1.0870
bond 63 68 360.00 1.4150
bond 63 76 360.00 1.4150
bond 65 66 384.00 1.4320
bond 65 68 384.00 1.4140
bond 66 67 389.50 1.0920
bond 66 68 320.00 1.5100
bond 66 72 380.00 1.5020
bond 67 68 389.50 1.0920
bond 68 68 320.00 1.5100
bond 68 69 384.00 1.4100
bond 68 71 384.00 1.4100
bond 68 87 384.00 1.4100
bond 69 70 615.50 0.9710
bond 70 71 615.50 0.9710
bond 70 74 615.50 0.9710
bond 70 86 615.50 0.9710
bond 70 87 615.50 0.9710
bond 71 84 320.00 1.6060
bond 72 73 398.50 1.0920
bond 72 74 484.00 1.4100
bond 72 86 484.00 1.4100
bond 74 84 320.00 1.6060
bond 75 76 320.00 1.5100
bond 75 77 384.00 1.4320
bond 75 78 389.50 1.0920
bond 75 79 380.00 1.5020
bond 76 76 320.00 1.5100
bond 76 77 384.00 1.4140
bond 76 78 389.50 1.0920
bond 76 80 384.00 1.4100
bond 76 88 384.00 1.4100
bond 79 82 398.50 1.0920
bond 79 83 484.00 1.4100
bond 79 89 484.00 1.4100
bond 80 81 615.50 0.9710
bond 80 84 320.00 1.6060
bond 81 83 615.50 0.9710
bond 81 88 615.50 0.9710
bond 81 89 615.50 0.9710
bond 83 84 320.00 1.6060
bond 84 85 700.00 1.4960
bond 90 91 556.85 0.9572
################################
## ##
## Angle Bending Parameters ##
## ##
################################
anglep 2 1 3 50.00 122.00
anglep 2 1 4 32.00 117.00
anglep 3 1 4 36.00 121.00
anglep 3 1 7 50.00 122.00
anglep 3 1 40 50.00 121.00
anglep 4 1 4 29.50 123.00
anglep 4 1 7 32.00 117.00
anglep 4 1 8 13.70 122.40
anglep 4 1 39 41.70 120.50
anglep 4 1 40 32.00 117.00
anglep 8 1 39 52.50 120.40
angle 1 2 3 55.00 109.80
angle 1 2 6 55.00 111.00
angle 1 2 30 61.00 109.60
angle 1 2 32 61.00 109.60
angle 3 2 6 39.00 109.50
angle 3 2 41 75.20 110.70
angle 6 2 6 40.00 107.60
angle 6 2 30 39.00 109.50
angle 6 2 32 39.00 109.50
angle 6 2 41 59.00 109.30
anglep 1 3 2 70.00 113.40
anglep 1 3 5 77.00 124.20
anglep 1 3 7 70.00 113.40
anglep 1 3 8 70.00 113.40
anglep 1 3 40 41.00 113.40
anglep 2 3 5 80.00 122.40
anglep 2 3 15 70.00 113.40
anglep 5 3 7 80.00 122.40
anglep 5 3 8 80.00 122.40
anglep 5 3 15 77.00 124.20
anglep 5 3 40 80.00 122.40
anglep 7 3 15 70.00 113.40
anglep 15 3 40 41.00 113.40
angle 1 7 3 61.00 109.60
angle 1 7 6 55.00 111.00
angle 1 7 7 54.00 111.30
angle 1 7 8 54.00 111.30
angle 1 7 30 61.00 109.60
angle 1 7 32 61.00 109.60
angle 3 7 6 39.00 109.50
angle 3 7 7 58.00 110.60
angle 3 7 8 58.00 110.60
angle 3 7 15 61.00 109.60
angle 3 7 16 58.00 110.60
angle 3 7 41 75.20 110.70
angle 6 7 7 42.00 110.70
angle 6 7 8 42.00 112.80
angle 6 7 10 59.00 110.00 108.90 108.70
angle 6 7 15 55.00 111.00
angle 6 7 16 42.00 112.80
angle 6 7 30 39.00 109.50
angle 6 7 32 39.00 109.50
angle 6 7 41 59.00 109.30
angle 7 7 8 48.20 109.50 110.20 111.00
angle 7 7 10 59.70 107.50
angle 7 7 30 58.00 110.60
angle 7 7 41 56.10 108.50
angle 8 7 8 48.20 109.50 110.20 111.00
angle 8 7 10 59.70 107.50
angle 8 7 30 58.00 110.60
angle 8 7 32 58.00 110.60
angle 8 7 41 75.20 110.70
angle 15 7 16 54.00 104.00
angle 15 7 30 61.00 109.60
angle 16 7 30 58.00 110.60
angle 16 7 41 54.00 104.00
angle 1 8 8 56.10 109.50
angle 1 8 9 54.60 111.00
angle 3 8 7 47.60 110.60
angle 3 8 8 47.60 110.60
angle 3 8 9 39.00 109.50
angle 7 8 7 48.20 109.50 110.20 111.00
angle 7 8 8 48.20 109.50 110.20 111.00
angle 7 8 9 42.00 110.70
angle 7 8 10 59.70 107.50
angle 7 8 12 53.20 108.00 109.50 110.10
angle 7 8 14 53.20 108.00 109.50 110.10
angle 7 8 17 38.90 110.60
angle 7 8 22 48.20 109.50 110.20 111.00
angle 7 8 26 38.80 112.70
angle 7 8 30 47.60 110.60
angle 7 8 32 47.60 110.60
angle 7 8 36 48.20 109.50 110.20 111.00
angle 8 8 8 48.20 109.50 110.20 111.00
angle 8 8 9 42.00 110.70
angle 8 8 12 53.20 108.00 109.50 110.10
angle 8 8 30 47.60 110.60
angle 8 8 32 47.60 110.60
angle 8 8 36 48.20 109.50 110.20 111.00
angle 8 8 37 56.10 109.50
angle 9 8 9 40.00 107.80
angle 9 8 10 59.00 110.00 108.90 108.70
angle 9 8 12 53.20 110.80 110.80 108.00
angle 9 8 14 53.20 110.80 110.80 108.00
angle 9 8 17 39.60 109.50 109.30 110.40
angle 9 8 22 61.20 109.80 109.30 110.70
angle 9 8 26 39.60 109.50
angle 9 8 30 39.00 109.50
angle 9 8 32 39.00 109.50
angle 9 8 36 42.00 110.70
angle 9 8 37 59.00 109.30
angle 36 8 37 56.10 109.50
angle 7 10 11 54.00 106.80
angle 8 10 11 54.00 106.80
angle 8 12 8 60.40 95.90
angle 8 12 12 71.90 101.80
angle 8 12 13 46.80 96.00
anglep 3 15 7 50.00 122.00
anglep 3 15 16 50.00 122.00
anglep 7 15 16 54.70 112.50
angle 6 16 6 40.00 107.80
angle 6 16 15 55.00 111.00
angle 6 16 16 42.00 110.70
angle 6 16 41 55.00 111.00
angle 7 16 9 42.00 110.70
angle 7 16 16 48.20 104.00
angle 9 16 9 40.00 107.80
angle 9 16 16 42.00 110.70
angle 15 16 16 54.00 104.00
angle 16 16 16 48.20 104.00
angle 16 16 41 54.00 104.00
anglep 8 17 17 33.80 122.30
anglep 17 17 17 54.70 121.70
anglep 17 17 18 35.30 120.00 120.50 0.00
anglep 17 17 19 43.20 120.00
anglep 17 17 21 60.00 123.57
angle 17 19 20 25.90 109.00
anglep 8 22 22 61.90 127.00
anglep 22 22 22 63.30 120.00
anglep 22 22 23 35.30 128.00
anglep 22 22 24 47.50 109.00
anglep 23 22 24 86.30 122.50
anglep 22 24 22 86.30 109.00
anglep 22 24 25 35.30 125.50
anglep 25 24 26 35.30 125.50
anglep 25 24 28 35.30 125.50
anglep 26 24 28 86.30 110.80
anglep 8 26 24 36.00 122.00
anglep 8 26 26 36.00 131.00
anglep 8 26 29 36.00 122.00
anglep 24 26 26 47.50 104.70
anglep 24 26 27 38.10 122.50
anglep 24 26 29 28.80 111.50
anglep 26 26 27 35.30 128.00
anglep 26 26 29 47.50 110.50