Le Mardi 21 Mai 2002 16:46, vous avez écrit :
> Hi everyone,
> I need to add hydrogen bonds in a pdb files (list of ...), so i want to use
> protonate in order to have good postitionning of the desired atoms.
> But protonate fails to add hydrogens to thymine.
> I have AMBER 6.
> I checkd the bugfixes, but except the PROTON8INFO location, i couldn't see
> what was wrong/corrected. Here is my pdb file :
> ATOM 157 P DA A 6 14.080 12.041 15.115
> ATOM 158 O1P DA A 6 13.288 11.118 15.952
> ATOM 159 O2P DA A 6 14.961 11.496 14.055
> ATOM 160 O5' DA A 6 13.083 13.098 14.473
> ATOM 161 C5' DA A 6 12.245 13.885 15.322
> ATOM 164 C4' DA A 6 11.340 14.769 14.501
> ATOM 166 O4' DA A 6 12.048 15.925 14.008
> ATOM 167 C3' DA A 6 10.676 14.117 13.295
> ATOM 169 O3' DA A 6 9.299 14.463 13.314
> ATOM 170 C2' DA A 6 11.417 14.719 12.105
> ATOM 173 C1' DA A 6 11.847 16.087 12.615
> ATOM 175 N9 DA A 6 13.094 16.617 12.058
> ATOM 176 C8 DA A 6 14.283 15.955 11.881
> ATOM 178 N7 DA A 6 15.237 16.706 11.386
> ATOM 179 C5 DA A 6 14.636 17.944 11.216
> ATOM 180 C6 DA A 6 15.120 19.172 10.723
> ATOM 181 N6 DA A 6 16.373 19.356 10.297
> ATOM 184 N1 DA A 6 14.262 20.216 10.682
> ATOM 185 C2 DA A 6 13.009 20.029 11.109
> ATOM 187 N3 DA A 6 12.437 18.924 11.594
> ATOM 188 C4 DA A 6 13.315 17.905 11.622
> ATOM 189 P DT A 7 8.327 13.943 12.158
> ATOM 190 O1P DT A 7 6.992 13.730 12.750
> ATOM 191 O2P DT A 7 8.971 12.852 11.385
> ATOM 192 O5' DT A 7 8.221 15.223 11.230
> ATOM 193 C5' DT A 7 7.944 16.491 11.827
> ATOM 194 C4' DT A 7 7.931 17.575 10.783
> ATOM 195 O4' DT A 7 9.265 18.016 10.437
> ATOM 196 C3' DT A 7 7.219 17.237 9.475
> ATOM 197 O3' DT A 7 6.320 18.307 9.191
> ATOM 198 C2' DT A 7 8.354 17.149 8.461
> ATOM 199 C1' DT A 7 9.373 18.127 9.026
> ATOM 200 N1 DT A 7 10.788 17.901 8.657
> ATOM 201 C2 DT A 7 11.526 19.000 8.248
> ATOM 202 O2 DT A 7 11.066 20.133 8.171
> ATOM 203 N3 DT A 7 12.830 18.725 7.928
> ATOM 204 C4 DT A 7 13.463 17.504 7.968
> ATOM 205 O4 DT A 7 14.649 17.423 7.649
> ATOM 206 C5 DT A 7 12.636 16.393 8.402
> ATOM 207 C6 DT A 7 11.356 16.645 8.720
> ATOM 208 P DT A 8 5.251 18.177 7.999
> ATOM 209 O1P DT A 8 3.951 18.607 8.576
> ATOM 210 O2P DT A 8 5.361 16.850 7.331
> ATOM 211 O5' DT A 8 5.750 19.315 7.016
> ATOM 212 C5' DT A 8 6.187 20.560 7.559
> ATOM 213 C4' DT A 8 6.963 21.345 6.534
> ATOM 214 O4' DT A 8 8.361 20.981 6.440
> ATOM 215 C3' DT A 8 6.398 21.320 5.118
> ATOM 216 O3' DT A 8 6.247 22.665 4.690
> ATOM 217 C2' DT A 8 7.468 20.596 4.315
> ATOM 218 C1' DT A 8 8.739 20.944 5.071
> ATOM 219 N1 DT A 8 9.839 19.978 4.929
> ATOM 220 C2 DT A 8 11.073 20.464 4.561
> ATOM 221 O2 DT A 8 11.288 21.649 4.341
> ATOM 222 N3 DT A 8 12.056 19.511 4.461
> ATOM 223 C4 DT A 8 11.928 18.154 4.691
> ATOM 224 O4 DT A 8 12.906 17.427 4.582
> ATOM 225 C5 DT A 8 10.602 17.713 5.061
> ATOM 226 C6 DT A 8 9.637 18.635 5.159
> ATOM 227 P DC A 9 5.839 22.984 3.181
> ATOM 228 O1P DC A 9 4.876 24.106 3.265
> ATOM 229 O2P DC A 9 5.461 21.734 2.469
> ATOM 230 O5' DC A 9 7.201 23.524 2.561
> ATOM 231 C5' DC A 9 7.951 24.536 3.247
> ATOM 234 C4' DC A 9 9.128 24.974 2.412
> ATOM 236 O4' DC A 9 10.120 23.930 2.372
> ATOM 237 C3' DC A 9 8.814 25.325 0.958
> ATOM 239 O3' DC A 9 9.616 26.459 0.613
> ATOM 240 C2' DC A 9 9.262 24.085 0.194
> ATOM 243 C1' DC A 9 10.421 23.574 1.032
> ATOM 245 N1 DC A 9 10.665 22.123 1.018
> ATOM 246 C2 DC A 9 11.949 21.661 0.715
> ATOM 247 O2 DC A 9 12.832 22.480 0.419
> ATOM 248 N3 DC A 9 12.199 20.335 0.752
> ATOM 249 C4 DC A 9 11.224 19.481 1.067
> ATOM 250 N4 DC A 9 11.527 18.178 1.106
> ATOM 253 C5 DC A 9 9.901 19.921 1.359
> ATOM 255 C6 DC A 9 9.667 21.239 1.323
> ATOM 257 P DG A 10 9.159 27.449 -0.568
> ATOM 258 O1P DG A 10 9.690 28.782 -0.195
> ATOM 259 O2P DG A 10 7.720 27.293 -0.890
> ATOM 260 O5' DG A 10 9.997 26.909 -1.807
> ATOM 261 C5' DG A 10 11.430 26.918 -1.768
> ATOM 264 C4' DG A 10 11.984 26.005 -2.835
> ATOM 266 O4' DG A 10 11.878 24.621 -2.436
> ATOM 267 C3' DG A 10 11.271 26.115 -4.189
> ATOM 269 O3' DG A 10 12.251 25.952 -5.213
> ATOM 270 C2' DG A 10 10.413 24.866 -4.231
> ATOM 273 C1' DG A 10 11.374 23.924 -3.555
> ATOM 275 N9 DG A 10 10.884 22.628 -3.123
> ATOM 276 C8 DG A 10 9.602 22.261 -2.802
> ATOM 278 N7 DG A 10 9.505 21.002 -2.471
> ATOM 279 C5 DG A 10 10.803 20.519 -2.582
> ATOM 280 C6 DG A 10 11.326 19.228 -2.355
> ATOM 281 O6 DG A 10 10.726 18.208 -2.001
> ATOM 282 N1 DG A 10 12.699 19.183 -2.582
> ATOM 284 C2 DG A 10 13.466 20.243 -2.979
> ATOM 285 N2 DG A 10 14.771 20.005 -3.147
> ATOM 288 N3 DG A 10 12.990 21.452 -3.194
> ATOM 289 C4 DG A 10 11.661 21.516 -2.978
>
> if you do :
> protonate -i mypdbfile -o mypdbfilewithH -d /whereislocatedPROTON_INFO,
> you get hydrogens for all residues except thymine (DT, i tried THY, T, ..).
>
> Can i have some help please. If someone has a fast and robust method to do
> it, i can sign for it, but i tried before to trust EDIT (from PLEP), but it
> wasn't robust enough.
>
> I intend to use this in a script, so i don't want to use xleap for that.
> Protonate sounded perfect, but i'm may be missing something.
> Thanks in advance,
> Stef
Received on Wed May 22 2002 - 04:41:08 PDT
