[gmx-users] problem with distance restraints
map110+ at pitt.edu
map110+ at pitt.edu
Sun Nov 23 16:15:35 CET 2008
Thanks for the fast reply! So the index is the residue number, and I can
get that from the pdb file right? And the numbers for the atom pairs, I'm
assuming, should be coming from the topology file. But for each atom pair,
should the low up1 and up2 columns always be equal to 0.0, 0.3, 0.8? Why
is low 0.0...instead of the distance between the atoms that you want to
restrain?
Thanks for your help again!
Maria
> You do not need so many distance restraints, it is enough to restraint the
> distance between the "O" atom of residue "i" and the "H" atom of the
> residue
> "i+4". Once you have the index for those atoms your [distance_restraints]
> section will have one of these lines
>
> ai aj 1 i 1 0.0 0.3 0.8 1
>
> for each pair of (i, i+4) residues and, if you use it correctly in the mdp
> and top files, you should have your helix even starting from a stretched
> structure... The folding time will depend on your sequence and I guess you
> will not obtain helices for some sequences even with these restraints but
> if
> you test this for a polyalanine of 20 residues in vacuum you will have
> your
> helix in less than 100 ps (a couple of minutes in your pc)
>
> Good luck,
>
> Angel.
>
>
>
> -----Mensaje original-----
> De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> En
> nombre de map110+ at pitt.edu
> Enviado el: domingo, 23 de noviembre de 2008 12:20 a.m.
> Para: gmx-users at gromacs.org
> Asunto: [gmx-users] problem with distance restraints
>
> Dear All,
>
> I am a new GROMACS user hoping to implement distance restraints on a
> peptide fragment so that given any starting conformation of the peptide,
> after 1 ns, the peptide will adopt the helical conformation. I'm starting
> with a coil conformation and I have added distance restraints to the
> topology file (atom pairs within a cutoff of 0.55 nm).
>
> [distance_restraints]
> ;ai aj type index type' low up1 up2 fac
> 1 13 1 0 1 0.35 0.40 0.45 1.0
> 1 15 1 1 1 0.47 0.52 0.57 1.0
> 1 16 1 2 1 0.53 0.58 0.63 1.0
> 1 19 1 3 1 0.47 0.52 0.57 1.0
> 1 13 1 4 1 0.37 0.42 0.47 1.0
> 1 15 1 5 1 0.47 0.52 0.57 1.0
> 1 16 1 6 1 0.51 0.56 0.61 1.0
> 1 19 1 7 1 0.43 0.48 0.53 1.0
> 5 13 1 8 1 0.24 0.29 0.34 1.0
> 5 15 1 9 1 0.38 0.43 0.48 1.0
> 5 20 1 10 1 0.48 0.53 0.58 1.0
> 5 16 1 11 1 0.47 0.52 0.57 1.0
> 5 17 1 12 1 0.50 0.55 0.60 1.0
> 5 19 1 13 1 0.45 0.50 0.55 1.0
> 11 13 1 14 1 0.13 0.18 0.23 1.0
> 11 15 1 15 1 0.24 0.29 0.34 1.0
> 11 20 1 16 1 0.36 0.41 0.46 1.0
> 11 21 1 17 1 0.46 0.51 0.56 1.0
> 11 16 1 18 1 0.34 0.39 0.44 1.0
> 11 17 1 19 1 0.40 0.45 0.50 1.0
> 11 19 1 20 1 0.34 0.39 0.44 1.0
> 12 13 1 21 1 0.21 0.26 0.31 1.0
> 12 15 1 22 1 0.25 0.30 0.35 1.0
> 12 20 1 23 1 0.38 0.43 0.48 1.0
> 12 21 1 24 1 0.46 0.51 0.56 1.0
> 12 16 1 25 1 0.35 0.40 0.45 1.0
> 12 17 1 26 1 0.45 0.50 0.55 1.0
> 12 19 1 27 1 0.33 0.38 0.43 1.0
> 6 13 1 28 1 0.34 0.39 0.44 1.0
> 6 15 1 29 1 0.47 0.52 0.57 1.0
> 6 20 1 30 1 0.53 0.58 0.63 1.0
> 7 13 1 31 1 0.46 0.51 0.56 1.0
> 5 22 1 32 1 0.47 0.52 0.57 1.0
> 11 22 1 33 1 0.38 0.43 0.48 1.0
> 11 24 1 34 1 0.52 0.57 0.62 1.0
> 12 22 1 35 1 0.44 0.49 0.54 1.0
> 6 22 1 36 1 0.51 0.56 0.61 1.0
> 5 39 1 37 1 0.52 0.57 0.62 1.0
> 5 42 1 38 1 0.51 0.56 0.61 1.0
> 5 43 1 39 1 0.51 0.56 0.61 1.0
> 11 39 1 40 1 0.48 0.53 0.58 1.0
> 11 42 1 41 1 0.53 0.58 0.63 1.0
> 12 39 1 42 1 0.53 0.58 0.63 1.0
> 6 39 1 43 1 0.49 0.54 0.59 1.0
> 6 41 1 44 1 0.51 0.56 0.61 1.0
> 6 46 1 45 1 0.54 0.59 0.64 1.0
> 6 42 1 46 1 0.42 0.47 0.52 1.0
> 6 43 1 47 1 0.44 0.49 0.54 1.0
> 7 42 1 48 1 0.43 0.48 0.53 1.0
> 7 43 1 49 1 0.42 0.47 0.52 1.0
> 8 41 1 50 1 0.54 0.59 0.64 1.0
> 8 42 1 51 1 0.40 0.45 0.50 1.0
> 8 43 1 52 1 0.42 0.47 0.52 1.0
> 9 41 1 53 1 0.50 0.55 0.60 1.0
> 9 45 1 54 1 0.52 0.57 0.62 1.0
> 9 46 1 55 1 0.51 0.56 0.61 1.0
> 9 42 1 56 1 0.37 0.42 0.47 1.0
> 9 43 1 57 1 0.43 0.48 0.53 1.0
> 10 42 1 58 1 0.47 0.52 0.57 1.0
> 10 43 1 59 1 0.46 0.51 0.56 1.0
> 6 85 1 60 1 0.52 0.57 0.62 1.0
> 7 85 1 61 1 0.53 0.58 0.63 1.0
> 8 84 1 62 1 0.51 0.56 0.61 1.0
> 8 85 1 63 1 0.41 0.46 0.51 1.0
> 9 65 1 64 1 0.49 0.54 0.59 1.0
> 9 67 1 65 1 0.49 0.54 0.59 1.0
> 9 84 1 66 1 0.40 0.45 0.50 1.0
> 9 85 1 67 1 0.29 0.34 0.39 1.0
> 9 68 1 68 1 0.49 0.54 0.59 1.0
> 10 84 1 69 1 0.54 0.59 0.64 1.0
> 10 85 1 70 1 0.46 0.51 0.56 1.0
> 10 68 1 71 1 0.52 0.57 0.62 1.0
> 9 86 1 72 1 0.49 0.54 0.59 1.0
> 9 88 1 73 1 0.48 0.53 0.58 1.0
> 9 97 1 74 1 0.53 0.58 0.63 1.0
> 8 99 1 75 1 0.54 0.59 0.64 1.0
> 8 102 1 76 1 0.55 0.60 0.65 1.0
> 8 103 1 77 1 0.53 0.58 0.63 1.0
> 8 104 1 78 1 0.51 0.56 0.61 1.0
> 9 99 1 79 1 0.46 0.51 0.56 1.0
> 9 102 1 80 1 0.53 0.58 0.63 1.0
> 9 103 1 81 1 0.51 0.56 0.61 1.0
> 9 104 1 82 1 0.53 0.58 0.63 1.0
> 10 103 1 83 1 0.50 0.55 0.60 1.0
> 10 104 1 84 1 0.46 0.51 0.56 1.0
> 1 111 1 85 1 0.54 0.59 0.64 1.0
> 1 113 1 86 1 0.49 0.54 0.59 1.0
> 1 111 1 87 1 0.47 0.52 0.57 1.0
> 1 112 1 88 1 0.51 0.56 0.61 1.0
> 1 113 1 89 1 0.45 0.50 0.55 1.0
> 1 120 1 90 1 0.44 0.49 0.54 1.0
> 1 121 1 91 1 0.44 0.49 0.54 1.0
> 1 117 1 92 1 0.51 0.56 0.61 1.0
> 1 119 1 93 1 0.49 0.54 0.59 1.0
> 1 120 1 94 1 0.36 0.41 0.46 1.0
> 1 121 1 95 1 0.36 0.41 0.46 1.0
> 5 120 1 96 1 0.46 0.51 0.56 1.0
> 5 121 1 97 1 0.49 0.54 0.59 1.0
> 11 119 1 98 1 0.52 0.57 0.62 1.0
> 11 120 1 99 1 0.41 0.46 0.51 1.0
> 11 121 1 100 1 0.48 0.53 0.58 1.0
> 12 117 1 101 1 0.53 0.58 0.63 1.0
> 12 118 1 102 1 0.54 0.59 0.64 1.0
> 12 119 1 103 1 0.41 0.46 0.51 1.0
> 12 120 1 104 1 0.31 0.36 0.41 1.0
> 12 121 1 105 1 0.40 0.45 0.50 1.0
> 6 120 1 106 1 0.45 0.50 0.55 1.0
> 6 121 1 107 1 0.48 0.53 0.58 1.0
> 13 22 1 108 1 0.26 0.31 0.36 1.0
> 13 24 1 109 1 0.41 0.46 0.51 1.0
> 13 37 1 110 1 0.47 0.52 0.57 1.0
> 13 25 1 111 1 0.49 0.54 0.59 1.0
> 13 26 1 112 1 0.51 0.56 0.61 1.0
> 13 27 1 113 1 0.48 0.53 0.58 1.0
> 15 22 1 114 1 0.24 0.29 0.34 1.0
> 15 24 1 115 1 0.38 0.43 0.48 1.0
> 15 37 1 116 1 0.47 0.52 0.57 1.0
> 15 25 1 117 1 0.47 0.52 0.57 1.0
> 15 26 1 118 1 0.47 0.52 0.57 1.0
> 15 27 1 119 1 0.46 0.51 0.56 1.0
> 15 29 1 120 1 0.54 0.59 0.64 1.0
> 15 31 1 121 1 0.52 0.57 0.62 1.0
> 20 22 1 122 1 0.13 0.18 0.23 1.0
> 20 24 1 123 1 0.24 0.29 0.34 1.0
> 20 37 1 124 1 0.35 0.40 0.45 1.0
> 20 38 1 125 1 0.47 0.52 0.57 1.0
> 20 25 1 126 1 0.35 0.40 0.45 1.0
> 20 26 1 127 1 0.36 0.41 0.46 1.0
> 20 27 1 128 1 0.39 0.44 0.49 1.0
> 20 29 1 129 1 0.42 0.47 0.52 1.0
> 20 31 1 130 1 0.47 0.52 0.57 1.0
> 20 33 1 131 1 0.50 0.55 0.60 1.0
> 20 35 1 132 1 0.52 0.57 0.62 1.0
> 21 22 1 133 1 0.22 0.27 0.32 1.0
> 21 24 1 134 1 0.27 0.32 0.37 1.0
> 21 37 1 135 1 0.38 0.43 0.48 1.0
> 21 38 1 136 1 0.49 0.54 0.59 1.0
> 21 25 1 137 1 0.38 0.43 0.48 1.0
> 21 26 1 138 1 0.38 0.43 0.48 1.0
> 21 27 1 139 1 0.44 0.49 0.54 1.0
> 21 29 1 140 1 0.40 0.45 0.50 1.0
> 21 31 1 141 1 0.50 0.55 0.60 1.0
> 21 33 1 142 1 0.47 0.52 0.57 1.0
> 21 35 1 143 1 0.52 0.57 0.62 1.0
> 16 22 1 144 1 0.34 0.39 0.44 1.0
> 16 24 1 145 1 0.46 0.51 0.56 1.0
> 16 25 1 146 1 0.52 0.57 0.62 1.0
> 16 26 1 147 1 0.47 0.52 0.57 1.0
> 16 27 1 148 1 0.43 0.48 0.53 1.0
> 16 29 1 149 1 0.53 0.58 0.63 1.0
> 16 31 1 150 1 0.45 0.50 0.55 1.0
> 16 33 1 151 1 0.54 0.59 0.64 1.0
> 16 35 1 152 1 0.51 0.56 0.61 1.0
> 17 22 1 153 1 0.33 0.38 0.43 1.0
> 17 24 1 154 1 0.44 0.49 0.54 1.0
> 17 25 1 155 1 0.45 0.50 0.55 1.0
> 17 26 1 156 1 0.38 0.43 0.48 1.0
> 17 27 1 157 1 0.31 0.36 0.41 1.0
> 17 29 1 158 1 0.45 0.50 0.55 1.0
> 17 31 1 159 1 0.32 0.37 0.42 1.0
> 17 33 1 160 1 0.46 0.51 0.56 1.0
> 17 35 1 161 1 0.40 0.45 0.50 1.0
> 19 22 1 162 1 0.47 0.52 0.57 1.0
> 19 27 1 163 1 0.55 0.60 0.65 1.0
> 13 39 1 164 1 0.42 0.47 0.52 1.0
> 13 41 1 165 1 0.54 0.59 0.64 1.0
> 13 42 1 166 1 0.53 0.58 0.63 1.0
> 13 43 1 167 1 0.53 0.58 0.63 1.0
> 15 39 1 168 1 0.44 0.49 0.54 1.0
> 20 39 1 169 1 0.35 0.40 0.45 1.0
> 20 41 1 170 1 0.49 0.54 0.59 1.0
> 20 45 1 171 1 0.54 0.59 0.64 1.0
> 20 46 1 172 1 0.50 0.55 0.60 1.0
> 21 39 1 173 1 0.40 0.45 0.50 1.0
> 21 41 1 174 1 0.53 0.58 0.63 1.0
> 21 46 1 175 1 0.51 0.56 0.61 1.0
> 13 120 1 176 1 0.52 0.57 0.62 1.0
> 15 120 1 177 1 0.54 0.59 0.64 1.0
> 22 39 1 178 1 0.27 0.32 0.37 1.0
> 22 41 1 179 1 0.41 0.46 0.51 1.0
> 22 45 1 180 1 0.49 0.54 0.59 1.0
> 22 46 1 181 1 0.48 0.53 0.58 1.0
> 22 42 1 182 1 0.47 0.52 0.57 1.0
> 22 43 1 183 1 0.47 0.52 0.57 1.0
> 24 39 1 184 1 0.24 0.29 0.34 1.0
> 24 41 1 185 1 0.38 0.43 0.48 1.0
> 24 45 1 186 1 0.47 0.52 0.57 1.0
> 24 46 1 187 1 0.48 0.53 0.58 1.0
> 24 42 1 188 1 0.47 0.52 0.57 1.0
> 24 43 1 189 1 0.47 0.52 0.57 1.0
> 37 39 1 190 1 0.13 0.18 0.23 1.0
> 37 41 1 191 1 0.24 0.29 0.34 1.0
> 37 45 1 192 1 0.34 0.39 0.44 1.0
> 37 46 1 193 1 0.39 0.44 0.49 1.0
> 37 42 1 194 1 0.35 0.40 0.45 1.0
> 37 43 1 195 1 0.36 0.41 0.46 1.0
> 38 39 1 196 1 0.21 0.26 0.31 1.0
> 38 41 1 197 1 0.25 0.30 0.35 1.0
> 38 45 1 198 1 0.36 0.41 0.46 1.0
> 38 46 1 199 1 0.43 0.48 0.53 1.0
> 38 42 1 200 1 0.37 0.42 0.47 1.0
> 38 43 1 201 1 0.37 0.42 0.47 1.0
> 25 39 1 202 1 0.36 0.41 0.46 1.0
> 25 41 1 203 1 0.48 0.53 0.58 1.0
> 25 43 1 204 1 0.53 0.58 0.63 1.0
> 26 39 1 205 1 0.49 0.54 0.59 1.0
> 37 47 1 206 1 0.43 0.48 0.53 1.0
> 38 47 1 207 1 0.41 0.46 0.51 1.0
> 38 49 1 208 1 0.54 0.59 0.64 1.0
> 38 52 1 209 1 0.55 0.60 0.65 1.0
> 39 47 1 210 1 0.36 0.41 0.46 1.0
> 39 49 1 211 1 0.48 0.53 0.58 1.0
> 39 50 1 212 1 0.54 0.59 0.64 1.0
> 41 47 1 213 1 0.24 0.29 0.34 1.0
> 41 49 1 214 1 0.38 0.43 0.48 1.0
> 41 54 1 215 1 0.48 0.53 0.58 1.0
> 41 50 1 216 1 0.46 0.51 0.56 1.0
> 41 51 1 217 1 0.51 0.56 0.61 1.0
> 41 52 1 218 1 0.48 0.53 0.58 1.0
> 45 47 1 219 1 0.13 0.18 0.23 1.0
> 45 49 1 220 1 0.24 0.29 0.34 1.0
> 45 54 1 221 1 0.36 0.41 0.46 1.0
> 45 55 1 222 1 0.48 0.53 0.58 1.0
> 45 50 1 223 1 0.34 0.39 0.44 1.0
> 45 51 1 224 1 0.41 0.46 0.51 1.0
> 45 52 1 225 1 0.41 0.46 0.51 1.0
> 45 53 1 226 1 0.51 0.56 0.61 1.0
> 46 47 1 227 1 0.22 0.27 0.32 1.0
> 46 49 1 228 1 0.27 0.32 0.37 1.0
> 46 54 1 229 1 0.40 0.45 0.50 1.0
> 46 55 1 230 1 0.50 0.55 0.60 1.0
> 46 50 1 231 1 0.36 0.41 0.46 1.0
> 46 51 1 232 1 0.47 0.52 0.57 1.0
> 46 52 1 233 1 0.49 0.54 0.59 1.0
> 42 47 1 234 1 0.33 0.38 0.43 1.0
> 42 49 1 235 1 0.46 0.51 0.56 1.0
> 42 54 1 236 1 0.52 0.57 0.62 1.0
> 43 47 1 237 1 0.45 0.50 0.55 1.0
> 41 56 1 238 1 0.46 0.51 0.56 1.0
> 45 56 1 239 1 0.37 0.42 0.47 1.0
> 45 58 1 240 1 0.51 0.56 0.61 1.0
> 46 56 1 241 1 0.43 0.48 0.53 1.0
> 42 56 1 242 1 0.46 0.51 0.56 1.0
> 45 65 1 243 1 0.53 0.58 0.63 1.0
> 45 85 1 244 1 0.52 0.57 0.62 1.0
> 46 85 1 245 1 0.50 0.55 0.60 1.0
> 42 65 1 246 1 0.54 0.59 0.64 1.0
> 42 85 1 247 1 0.50 0.55 0.60 1.0
> 45 92 1 248 1 0.50 0.55 0.60 1.0
> 45 93 1 249 1 0.43 0.48 0.53 1.0
> 46 91 1 250 1 0.46 0.51 0.56 1.0
> 46 92 1 251 1 0.40 0.45 0.50 1.0
> 46 93 1 252 1 0.31 0.36 0.41 1.0
> 47 56 1 253 1 0.27 0.32 0.37 1.0
> 47 58 1 254 1 0.41 0.46 0.51 1.0
> 47 63 1 255 1 0.49 0.54 0.59 1.0
> 47 59 1 256 1 0.47 0.52 0.57 1.0
> 47 60 1 257 1 0.48 0.53 0.58 1.0
> 49 56 1 258 1 0.24 0.29 0.34 1.0
> 49 58 1 259 1 0.38 0.43 0.48 1.0
> 49 63 1 260 1 0.46 0.51 0.56 1.0
> 49 64 1 261 1 0.55 0.60 0.65 1.0
> 49 59 1 262 1 0.48 0.53 0.58 1.0
> 49 60 1 263 1 0.50 0.55 0.60 1.0
> 54 56 1 264 1 0.13 0.18 0.23 1.0
> 54 58 1 265 1 0.24 0.29 0.34 1.0
> 54 63 1 266 1 0.32 0.37 0.42 1.0
> 54 64 1 267 1 0.41 0.46 0.51 1.0
> 54 59 1 268 1 0.36 0.41 0.46 1.0
> 54 60 1 269 1 0.40 0.45 0.50 1.0
> 54 61 1 270 1 0.55 0.60 0.65 1.0
> 54 62 1 271 1 0.44 0.49 0.54 1.0
> 55 56 1 272 1 0.21 0.26 0.31 1.0
> 55 58 1 273 1 0.25 0.30 0.35 1.0
> 55 63 1 274 1 0.32 0.37 0.42 1.0
> 55 64 1 275 1 0.37 0.42 0.47 1.0
> 55 59 1 276 1 0.39 0.44 0.49 1.0
> 55 60 1 277 1 0.44 0.49 0.54 1.0
> 55 62 1 278 1 0.44 0.49 0.54 1.0
> 50 56 1 279 1 0.36 0.41 0.46 1.0
> 50 58 1 280 1 0.48 0.53 0.58 1.0
> 51 56 1 281 1 0.38 0.43 0.48 1.0
> 51 58 1 282 1 0.48 0.53 0.58 1.0
> 51 59 1 283 1 0.55 0.60 0.65 1.0
> 51 60 1 284 1 0.50 0.55 0.60 1.0
> 51 62 1 285 1 0.50 0.55 0.60 1.0
> 52 56 1 286 1 0.31 0.36 0.41 1.0
> 52 58 1 287 1 0.40 0.45 0.50 1.0
> 52 63 1 288 1 0.54 0.59 0.64 1.0
> 52 59 1 289 1 0.45 0.50 0.55 1.0
> 52 60 1 290 1 0.38 0.43 0.48 1.0
> 52 61 1 291 1 0.50 0.55 0.60 1.0
> 52 62 1 292 1 0.39 0.44 0.49 1.0
> 53 56 1 293 1 0.50 0.55 0.60 1.0
> 47 65 1 294 1 0.48 0.53 0.58 1.0
> 47 85 1 295 1 0.54 0.59 0.64 1.0
> 49 65 1 296 1 0.46 0.51 0.56 1.0
> 49 85 1 297 1 0.54 0.59 0.64 1.0
> 54 65 1 298 1 0.36 0.41 0.46 1.0
> 54 67 1 299 1 0.49 0.54 0.59 1.0
> 54 84 1 300 1 0.52 0.57 0.62 1.0
> 54 85 1 301 1 0.52 0.57 0.62 1.0
> 55 65 1 302 1 0.39 0.44 0.49 1.0
> 55 67 1 303 1 0.51 0.56 0.61 1.0
> 47 92 1 304 1 0.52 0.57 0.62 1.0
> 47 93 1 305 1 0.47 0.52 0.57 1.0
> 49 91 1 306 1 0.52 0.57 0.62 1.0
> 49 92 1 307 1 0.43 0.48 0.53 1.0
> 49 93 1 308 1 0.41 0.46 0.51 1.0
> 54 92 1 309 1 0.48 0.53 0.58 1.0
> 54 93 1 310 1 0.51 0.56 0.61 1.0
> 55 92 1 311 1 0.51 0.56 0.61 1.0
> 50 92 1 312 1 0.49 0.54 0.59 1.0
> 50 93 1 313 1 0.46 0.51 0.56 1.0
> 56 65 1 314 1 0.28 0.33 0.38 1.0
> 56 67 1 315 1 0.42 0.47 0.52 1.0
> 56 84 1 316 1 0.47 0.52 0.57 1.0
> 56 85 1 317 1 0.48 0.53 0.58 1.0
> 56 68 1 318 1 0.52 0.57 0.62 1.0
> 56 69 1 319 1 0.54 0.59 0.64 1.0
> 56 70 1 320 1 0.52 0.57 0.62 1.0
> 58 65 1 321 1 0.24 0.29 0.34 1.0
> 58 67 1 322 1 0.38 0.43 0.48 1.0
> 58 84 1 323 1 0.48 0.53 0.58 1.0
> 58 85 1 324 1 0.52 0.57 0.62 1.0
> 58 68 1 325 1 0.46 0.51 0.56 1.0
> 58 69 1 326 1 0.46 0.51 0.56 1.0
> 58 70 1 327 1 0.42 0.47 0.52 1.0
> 58 72 1 328 1 0.54 0.59 0.64 1.0
> 58 73 1 329 1 0.49 0.54 0.59 1.0
> 63 65 1 330 1 0.13 0.18 0.23 1.0
> 63 67 1 331 1 0.24 0.29 0.34 1.0
> 63 84 1 332 1 0.36 0.41 0.46 1.0
> 63 85 1 333 1 0.42 0.47 0.52 1.0
> 63 68 1 334 1 0.33 0.38 0.43 1.0
> 63 69 1 335 1 0.34 0.39 0.44 1.0
> 63 70 1 336 1 0.35 0.40 0.45 1.0
> 63 72 1 337 1 0.42 0.47 0.52 1.0
> 63 73 1 338 1 0.43 0.48 0.53 1.0
> 63 75 1 339 1 0.47 0.52 0.57 1.0
> 63 76 1 340 1 0.50 0.55 0.60 1.0
> 64 65 1 341 1 0.22 0.27 0.32 1.0
> 64 67 1 342 1 0.27 0.32 0.37 1.0
> 64 84 1 343 1 0.40 0.45 0.50 1.0
> 64 85 1 344 1 0.49 0.54 0.59 1.0
> 64 68 1 345 1 0.35 0.40 0.45 1.0
> 64 69 1 346 1 0.33 0.38 0.43 1.0
> 64 70 1 347 1 0.36 0.41 0.46 1.0
> 64 72 1 348 1 0.37 0.42 0.47 1.0
> 64 73 1 349 1 0.41 0.46 0.51 1.0
> 64 75 1 350 1 0.42 0.47 0.52 1.0
> 64 76 1 351 1 0.44 0.49 0.54 1.0
> 64 78 1 352 1 0.51 0.56 0.61 1.0
> 64 80 1 353 1 0.52 0.57 0.62 1.0
> 59 65 1 354 1 0.31 0.36 0.41 1.0
> 59 67 1 355 1 0.45 0.50 0.55 1.0
> 59 68 1 356 1 0.48 0.53 0.58 1.0
> 59 69 1 357 1 0.44 0.49 0.54 1.0
> 59 70 1 358 1 0.37 0.42 0.47 1.0
> 59 72 1 359 1 0.54 0.59 0.64 1.0
> 59 73 1 360 1 0.43 0.48 0.53 1.0
> 59 75 1 361 1 0.52 0.57 0.62 1.0
> 60 65 1 362 1 0.46 0.51 0.56 1.0
> 60 70 1 363 1 0.50 0.55 0.60 1.0
> 60 73 1 364 1 0.54 0.59 0.64 1.0
> 61 65 1 365 1 0.55 0.60 0.65 1.0
> 61 70 1 366 1 0.51 0.56 0.61 1.0
> 61 73 1 367 1 0.54 0.59 0.64 1.0
> 62 65 1 368 1 0.54 0.59 0.64 1.0
> 63 86 1 369 1 0.44 0.49 0.54 1.0
> 64 86 1 370 1 0.46 0.51 0.56 1.0
> 65 86 1 371 1 0.35 0.40 0.45 1.0
> 65 88 1 372 1 0.48 0.53 0.58 1.0
> 65 90 1 373 1 0.52 0.57 0.62 1.0
> 65 91 1 374 1 0.55 0.60 0.65 1.0
> 67 86 1 375 1 0.24 0.29 0.34 1.0
> 67 88 1 376 1 0.38 0.43 0.48 1.0
> 67 97 1 377 1 0.47 0.52 0.57 1.0
> 67 98 1 378 1 0.53 0.58 0.63 1.0
> 67 89 1 379 1 0.48 0.53 0.58 1.0
> 67 90 1 380 1 0.48 0.53 0.58 1.0
> 67 91 1 381 1 0.53 0.58 0.63 1.0
> 84 86 1 382 1 0.13 0.18 0.23 1.0
> 84 88 1 383 1 0.24 0.29 0.34 1.0
> 84 97 1 384 1 0.34 0.39 0.44 1.0
> 84 98 1 385 1 0.42 0.47 0.52 1.0
> 84 89 1 386 1 0.35 0.40 0.45 1.0
> 84 90 1 387 1 0.38 0.43 0.48 1.0
> 84 91 1 388 1 0.41 0.46 0.51 1.0
> 84 92 1 389 1 0.50 0.55 0.60 1.0
> 85 86 1 390 1 0.21 0.26 0.31 1.0
> 85 88 1 391 1 0.25 0.30 0.35 1.0
> 85 97 1 392 1 0.35 0.40 0.45 1.0
> 85 98 1 393 1 0.46 0.51 0.56 1.0
> 85 89 1 394 1 0.38 0.43 0.48 1.0
> 85 90 1 395 1 0.39 0.44 0.49 1.0
> 85 91 1 396 1 0.38 0.43 0.48 1.0
> 85 92 1 397 1 0.48 0.53 0.58 1.0
> 85 93 1 398 1 0.53 0.58 0.63 1.0
> 68 86 1 399 1 0.33 0.38 0.43 1.0
> 68 88 1 400 1 0.46 0.51 0.56 1.0
> 68 97 1 401 1 0.50 0.55 0.60 1.0
> 69 86 1 402 1 0.46 0.51 0.56 1.0
> 72 86 1 403 1 0.53 0.58 0.63 1.0
> 76 86 1 404 1 0.52 0.57 0.62 1.0
> 67 99 1 405 1 0.51 0.56 0.61 1.0
> 84 99 1 406 1 0.38 0.43 0.48 1.0
> 84 101 1 407 1 0.51 0.56 0.61 1.0
> 84 103 1 408 1 0.51 0.56 0.61 1.0
> 85 99 1 409 1 0.36 0.41 0.46 1.0
> 85 101 1 410 1 0.50 0.55 0.60 1.0
> 85 102 1 411 1 0.53 0.58 0.63 1.0
> 85 103 1 412 1 0.50 0.55 0.60 1.0
> 68 99 1 413 1 0.52 0.57 0.62 1.0
> 68 103 1 414 1 0.50 0.55 0.60 1.0
> 68 105 1 415 1 0.53 0.58 0.63 1.0
> 85 123 1 416 1 0.55 0.60 0.65 1.0
> 86 99 1 417 1 0.33 0.38 0.43 1.0
> 86 101 1 418 1 0.46 0.51 0.56 1.0
> 86 102 1 419 1 0.53 0.58 0.63 1.0
> 86 103 1 420 1 0.51 0.56 0.61 1.0
> 86 105 1 421 1 0.54 0.59 0.64 1.0
> 88 99 1 422 1 0.24 0.29 0.34 1.0
> 88 101 1 423 1 0.38 0.43 0.48 1.0
> 88 106 1 424 1 0.46 0.51 0.56 1.0
> 88 107 1 425 1 0.53 0.58 0.63 1.0
> 88 102 1 426 1 0.48 0.53 0.58 1.0
> 88 103 1 427 1 0.50 0.55 0.60 1.0
> 88 105 1 428 1 0.55 0.60 0.65 1.0
> 97 99 1 429 1 0.13 0.18 0.23 1.0
> 97 101 1 430 1 0.24 0.29 0.34 1.0
> 97 106 1 431 1 0.33 0.38 0.43 1.0
> 97 107 1 432 1 0.39 0.44 0.49 1.0
> 97 102 1 433 1 0.36 0.41 0.46 1.0
> 97 103 1 434 1 0.40 0.45 0.50 1.0
> 97 104 1 435 1 0.54 0.59 0.64 1.0
> 97 105 1 436 1 0.43 0.48 0.53 1.0
> 98 99 1 437 1 0.22 0.27 0.32 1.0
> 98 101 1 438 1 0.27 0.32 0.37 1.0
> 98 106 1 439 1 0.35 0.40 0.45 1.0
> 98 107 1 440 1 0.38 0.43 0.48 1.0
> 98 102 1 441 1 0.40 0.45 0.50 1.0
> 98 103 1 442 1 0.44 0.49 0.54 1.0
> 98 105 1 443 1 0.43 0.48 0.53 1.0
> 89 99 1 444 1 0.36 0.41 0.46 1.0
> 89 101 1 445 1 0.48 0.53 0.58 1.0
> 89 106 1 446 1 0.53 0.58 0.63 1.0
> 90 99 1 447 1 0.49 0.54 0.59 1.0
> 91 99 1 448 1 0.51 0.56 0.61 1.0
> 88 108 1 449 1 0.51 0.56 0.61 1.0
> 97 108 1 450 1 0.40 0.45 0.50 1.0
> 97 110 1 451 1 0.52 0.57 0.62 1.0
> 97 115 1 452 1 0.52 0.57 0.62 1.0
> 98 108 1 453 1 0.45 0.50 0.55 1.0
> 86 123 1 454 1 0.52 0.57 0.62 1.0
> 88 122 1 455 1 0.50 0.55 0.60 1.0
> 88 123 1 456 1 0.38 0.43 0.48 1.0
> 97 117 1 457 1 0.54 0.59 0.64 1.0
> 97 122 1 458 1 0.51 0.56 0.61 1.0
> 97 123 1 459 1 0.39 0.44 0.49 1.0
> 98 123 1 460 1 0.44 0.49 0.54 1.0
> 89 122 1 461 1 0.46 0.51 0.56 1.0
> 89 123 1 462 1 0.34 0.39 0.44 1.0
> 90 122 1 463 1 0.50 0.55 0.60 1.0
> 90 123 1 464 1 0.40 0.45 0.50 1.0
> 91 122 1 465 1 0.45 0.50 0.55 1.0
> 91 123 1 466 1 0.36 0.41 0.46 1.0
> 91 120 1 467 1 0.55 0.60 0.65 1.0
> 92 123 1 468 1 0.48 0.53 0.58 1.0
> 93 123 1 469 1 0.52 0.57 0.62 1.0
> 88 126 1 470 1 0.54 0.59 0.64 1.0
> 88 132 1 471 1 0.53 0.58 0.63 1.0
> 89 124 1 472 1 0.49 0.54 0.59 1.0
> 89 126 1 473 1 0.43 0.48 0.53 1.0
> 89 132 1 474 1 0.41 0.46 0.51 1.0
> 89 133 1 475 1 0.46 0.51 0.56 1.0
> 89 127 1 476 1 0.55 0.60 0.65 1.0
> 90 124 1 477 1 0.53 0.58 0.63 1.0
> 90 126 1 478 1 0.44 0.49 0.54 1.0
> 90 132 1 479 1 0.37 0.42 0.47 1.0
> 90 133 1 480 1 0.41 0.46 0.51 1.0
> 91 124 1 481 1 0.48 0.53 0.58 1.0
> 91 126 1 482 1 0.43 0.48 0.53 1.0
> 91 132 1 483 1 0.33 0.38 0.43 1.0
> 91 133 1 484 1 0.32 0.37 0.42 1.0
> 92 126 1 485 1 0.51 0.56 0.61 1.0
> 92 132 1 486 1 0.38 0.43 0.48 1.0
> 92 133 1 487 1 0.34 0.39 0.44 1.0
> 93 132 1 488 1 0.42 0.47 0.52 1.0
> 93 133 1 489 1 0.34 0.39 0.44 1.0
> 88 134 1 490 1 0.54 0.59 0.64 1.0
> 88 137 1 491 1 0.53 0.58 0.63 1.0
> 89 134 1 492 1 0.40 0.45 0.50 1.0
> 89 136 1 493 1 0.45 0.50 0.55 1.0
> 89 137 1 494 1 0.41 0.46 0.51 1.0
> 89 138 1 495 1 0.45 0.50 0.55 1.0
> 89 139 1 496 1 0.49 0.54 0.59 1.0
> 89 140 1 497 1 0.49 0.54 0.59 1.0
> 90 134 1 498 1 0.33 0.38 0.43 1.0
> 90 136 1 499 1 0.34 0.39 0.44 1.0
> 90 143 1 500 1 0.49 0.54 0.59 1.0
> 90 137 1 501 1 0.28 0.33 0.38 1.0
> 90 138 1 502 1 0.34 0.39 0.44 1.0
> 90 139 1 503 1 0.41 0.46 0.51 1.0
> 90 140 1 504 1 0.39 0.44 0.49 1.0
> 91 134 1 505 1 0.33 0.38 0.43 1.0
> 91 136 1 506 1 0.32 0.37 0.42 1.0
> 91 143 1 507 1 0.47 0.52 0.57 1.0
> 91 137 1 508 1 0.30 0.35 0.40 1.0
> 91 138 1 509 1 0.42 0.47 0.52 1.0
> 91 139 1 510 1 0.49 0.54 0.59 1.0
> 91 140 1 511 1 0.48 0.53 0.58 1.0
> 92 134 1 512 1 0.35 0.40 0.45 1.0
> 92 136 1 513 1 0.27 0.32 0.37 1.0
> 92 143 1 514 1 0.40 0.45 0.50 1.0
> 92 137 1 515 1 0.25 0.30 0.35 1.0
> 92 138 1 516 1 0.39 0.44 0.49 1.0
> 92 139 1 517 1 0.48 0.53 0.58 1.0
> 92 140 1 518 1 0.45 0.50 0.55 1.0
> 92 140 1 519 1 0.51 0.56 0.61 1.0
> 93 134 1 520 1 0.43 0.48 0.53 1.0
> 93 136 1 521 1 0.35 0.40 0.45 1.0
> 93 143 1 522 1 0.45 0.50 0.55 1.0
> 93 137 1 523 1 0.37 0.42 0.47 1.0
> 93 138 1 524 1 0.52 0.57 0.62 1.0
> 99 108 1 525 1 0.30 0.35 0.40 1.0
> 99 110 1 526 1 0.43 0.48 0.53 1.0
> 99 115 1 527 1 0.46 0.51 0.56 1.0
> 99 116 1 528 1 0.52 0.57 0.62 1.0
> 99 111 1 529 1 0.53 0.58 0.63 1.0
> 101 108 1 530 1 0.24 0.29 0.34 1.0
> 101 110 1 531 1 0.38 0.43 0.48 1.0
> 101 115 1 532 1 0.45 0.50 0.55 1.0
> 101 116 1 533 1 0.50 0.55 0.60 1.0
> 101 111 1 534 1 0.49 0.54 0.59 1.0
> 101 112 1 535 1 0.52 0.57 0.62 1.0
> 106 108 1 536 1 0.13 0.18 0.23 1.0
> 106 110 1 537 1 0.24 0.29 0.34 1.0
> 106 115 1 538 1 0.31 0.36 0.41 1.0
> 106 116 1 539 1 0.36 0.41 0.46 1.0
> 106 111 1 540 1 0.37 0.42 0.47 1.0
> 106 112 1 541 1 0.42 0.47 0.52 1.0
> 106 114 1 542 1 0.46 0.51 0.56 1.0
> 107 108 1 543 1 0.21 0.26 0.31 1.0
> 107 110 1 544 1 0.25 0.30 0.35 1.0
> 107 115 1 545 1 0.30 0.35 0.40 1.0
> 107 116 1 546 1 0.31 0.36 0.41 1.0
> 107 111 1 547 1 0.40 0.45 0.50 1.0
> 107 112 1 548 1 0.46 0.51 0.56 1.0
> 107 114 1 549 1 0.47 0.52 0.57 1.0
> 102 108 1 550 1 0.29 0.34 0.39 1.0
> 102 110 1 551 1 0.43 0.48 0.53 1.0
> 102 115 1 552 1 0.53 0.58 0.63 1.0
> 102 111 1 553 1 0.49 0.54 0.59 1.0
> 102 112 1 554 1 0.48 0.53 0.58 1.0
> 102 114 1 555 1 0.54 0.59 0.64 1.0
> 103 108 1 556 1 0.44 0.49 0.54 1.0
> 104 108 1 557 1 0.52 0.57 0.62 1.0
> 105 108 1 558 1 0.52 0.57 0.62 1.0
> 99 117 1 559 1 0.48 0.53 0.58 1.0
> 99 122 1 560 1 0.51 0.56 0.61 1.0
> 99 123 1 561 1 0.41 0.46 0.51 1.0
> 99 121 1 562 1 0.49 0.54 0.59 1.0
> 101 117 1 563 1 0.50 0.55 0.60 1.0
> 101 123 1 564 1 0.49 0.54 0.59 1.0
> 101 121 1 565 1 0.52 0.57 0.62 1.0
> 106 117 1 566 1 0.39 0.44 0.49 1.0
> 106 118 1 567 1 0.51 0.56 0.61 1.0
> 106 122 1 568 1 0.49 0.54 0.59 1.0
> 106 123 1 569 1 0.44 0.49 0.54 1.0
> 106 121 1 570 1 0.44 0.49 0.54 1.0
> 107 117 1 571 1 0.41 0.46 0.51 1.0
> 107 118 1 572 1 0.51 0.56 0.61 1.0
> 107 122 1 573 1 0.50 0.55 0.60 1.0
> 107 123 1 574 1 0.46 0.51 0.56 1.0
> 107 121 1 575 1 0.49 0.54 0.59 1.0
> 108 117 1 576 1 0.31 0.36 0.41 1.0
> 108 118 1 577 1 0.44 0.49 0.54 1.0
> 108 122 1 578 1 0.46 0.51 0.56 1.0
> 108 123 1 579 1 0.43 0.48 0.53 1.0
> 108 119 1 580 1 0.52 0.57 0.62 1.0
> 108 120 1 581 1 0.46 0.51 0.56 1.0
> 108 121 1 582 1 0.33 0.38 0.43 1.0
> 110 117 1 583 1 0.24 0.29 0.34 1.0
> 110 118 1 584 1 0.38 0.43 0.48 1.0
> 110 122 1 585 1 0.44 0.49 0.54 1.0
> 110 123 1 586 1 0.45 0.50 0.55 1.0
> 110 119 1 587 1 0.48 0.53 0.58 1.0
> 110 120 1 588 1 0.44 0.49 0.54 1.0
> 110 121 1 589 1 0.30 0.35 0.40 1.0
> 115 117 1 590 1 0.13 0.18 0.23 1.0
> 115 118 1 591 1 0.24 0.29 0.34 1.0
> 115 122 1 592 1 0.31 0.36 0.41 1.0
> 115 123 1 593 1 0.34 0.39 0.44 1.0
> 115 119 1 594 1 0.36 0.41 0.46 1.0
> 115 120 1 595 1 0.36 0.41 0.46 1.0
> 115 121 1 596 1 0.26 0.31 0.36 1.0
> 116 117 1 597 1 0.22 0.27 0.32 1.0
> 116 118 1 598 1 0.27 0.32 0.37 1.0
> 116 122 1 599 1 0.30 0.35 0.40 1.0
> 116 123 1 600 1 0.35 0.40 0.45 1.0
> 116 119 1 601 1 0.41 0.46 0.51 1.0
> 116 120 1 602 1 0.45 0.50 0.55 1.0
> 116 121 1 603 1 0.37 0.42 0.47 1.0
> 111 117 1 604 1 0.28 0.33 0.38 1.0
> 111 118 1 605 1 0.42 0.47 0.52 1.0
> 111 122 1 606 1 0.52 0.57 0.62 1.0
> 111 123 1 607 1 0.54 0.59 0.64 1.0
> 111 119 1 608 1 0.48 0.53 0.58 1.0
> 111 120 1 609 1 0.42 0.47 0.52 1.0
> 111 121 1 610 1 0.27 0.32 0.37 1.0
> 112 117 1 611 1 0.43 0.48 0.53 1.0
> 112 120 1 612 1 0.55 0.60 0.65 1.0
> 112 121 1 613 1 0.40 0.45 0.50 1.0
> 113 117 1 614 1 0.51 0.56 0.61 1.0
> 113 121 1 615 1 0.45 0.50 0.55 1.0
> 114 117 1 616 1 0.52 0.57 0.62 1.0
> 114 121 1 617 1 0.52 0.57 0.62 1.0
> 115 124 1 618 1 0.41 0.46 0.51 1.0
> 115 126 1 619 1 0.51 0.56 0.61 1.0
> 116 124 1 620 1 0.37 0.42 0.47 1.0
> 116 126 1 621 1 0.47 0.52 0.57 1.0
> 116 127 1 622 1 0.54 0.59 0.64 1.0
> 116 128 1 623 1 0.50 0.55 0.60 1.0
> 117 124 1 624 1 0.36 0.41 0.46 1.0
> 117 126 1 625 1 0.48 0.53 0.58 1.0
> 117 133 1 626 1 0.53 0.58 0.63 1.0
> 118 124 1 627 1 0.24 0.29 0.34 1.0
> 118 126 1 628 1 0.38 0.43 0.48 1.0
> 118 132 1 629 1 0.45 0.50 0.55 1.0
> 118 133 1 630 1 0.42 0.47 0.52 1.0
> 118 127 1 631 1 0.49 0.54 0.59 1.0
> 118 128 1 632 1 0.51 0.56 0.61 1.0
> 122 124 1 633 1 0.13 0.18 0.23 1.0
> 122 126 1 634 1 0.24 0.29 0.34 1.0
> 122 132 1 635 1 0.31 0.36 0.41 1.0
> 122 133 1 636 1 0.31 0.36 0.41 1.0
> 122 127 1 637 1 0.37 0.42 0.47 1.0
> 122 128 1 638 1 0.41 0.46 0.51 1.0
> 123 124 1 639 1 0.21 0.26 0.31 1.0
> 123 126 1 640 1 0.25 0.30 0.35 1.0
> 123 132 1 641 1 0.30 0.35 0.40 1.0
> 123 133 1 642 1 0.32 0.37 0.42 1.0
> 123 127 1 643 1 0.40 0.45 0.50 1.0
> 123 128 1 644 1 0.45 0.50 0.55 1.0
> 119 124 1 645 1 0.33 0.38 0.43 1.0
> 119 126 1 646 1 0.46 0.51 0.56 1.0
> 119 132 1 647 1 0.48 0.53 0.58 1.0
> 119 133 1 648 1 0.42 0.47 0.52 1.0
> 120 124 1 649 1 0.43 0.48 0.53 1.0
> 120 126 1 650 1 0.54 0.59 0.64 1.0
> 120 133 1 651 1 0.48 0.53 0.58 1.0
> 121 124 1 652 1 0.47 0.52 0.57 1.0
> 122 134 1 653 1 0.43 0.48 0.53 1.0
> 122 136 1 654 1 0.54 0.59 0.64 1.0
> 123 134 1 655 1 0.40 0.45 0.50 1.0
> 123 136 1 656 1 0.50 0.55 0.60 1.0
> 124 134 1 657 1 0.37 0.42 0.47 1.0
> 124 136 1 658 1 0.49 0.54 0.59 1.0
> 126 134 1 659 1 0.24 0.29 0.34 1.0
> 126 136 1 660 1 0.38 0.43 0.48 1.0
> 126 143 1 661 1 0.46 0.51 0.56 1.0
> 126 137 1 662 1 0.48 0.53 0.58 1.0
> 126 138 1 663 1 0.52 0.57 0.62 1.0
> 126 139 1 664 1 0.47 0.52 0.57 1.0
> 126 139 1 665 1 0.45 0.50 0.55 1.0
> 132 134 1 666 1 0.13 0.18 0.23 1.0
> 132 136 1 667 1 0.24 0.29 0.34 1.0
> 132 143 1 668 1 0.34 0.39 0.44 1.0
> 132 137 1 669 1 0.36 0.41 0.46 1.0
> 132 138 1 670 1 0.43 0.48 0.53 1.0
> 132 139 1 671 1 0.41 0.46 0.51 1.0
> 132 140 1 672 1 0.55 0.60 0.65 1.0
> 132 140 1 673 1 0.35 0.40 0.45 1.0
> 133 134 1 674 1 0.22 0.27 0.32 1.0
> 133 136 1 675 1 0.27 0.32 0.37 1.0
> 133 143 1 676 1 0.36 0.41 0.46 1.0
> 133 137 1 677 1 0.39 0.44 0.49 1.0
> 133 138 1 678 1 0.49 0.54 0.59 1.0
> 133 139 1 679 1 0.49 0.54 0.59 1.0
> 133 139 1 680 1 0.40 0.45 0.50 1.0
> 127 134 1 681 1 0.30 0.35 0.40 1.0
> 127 136 1 682 1 0.43 0.48 0.53 1.0
> 127 143 1 683 1 0.47 0.52 0.57 1.0
> 127 137 1 684 1 0.54 0.59 0.64 1.0
> 127 138 1 685 1 0.55 0.60 0.65 1.0
> 127 139 1 686 1 0.47 0.52 0.57 1.0
> 127 139 1 687 1 0.41 0.46 0.51 1.0
> 128 134 1 688 1 0.44 0.49 0.54 1.0
> 128 134 1 689 1 0.55 0.60 0.65 1.0
> 129 134 1 690 1 0.53 0.58 0.63 1.0
> 130 134 1 691 1 0.55 0.60 0.65 1.0
> 130 134 1 692 1 0.54 0.59 0.64 1.0
>
>>From the mailing list archives, it seems that the distance I want to
> restrain the atoms to should be in the low column while the up1 and up2
> values are being arbitrarily assigned. I have run several simulations with
> different up1 and up2 values and in this case, up1 is +0.05 and up2 +0.10.
> However, none of the simulations have been able to change the conformation
> of the peptide fragment to the desired form. So, it seems that my distance
> restraints aren't working properly.
>
> I'm using the GROMOS force field and the spc water model. I'm also running
> the parallelized version of mdrun.
>
> Does anyone have any suggestions/comments?
>
> Thanks for your help in advance!
>
> Maria
>
>
> _______________________________________________
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