I'd like to do a PDB2PQR run of my protein with its 'ligands' - actually substrates & am having problems getting the server to recognize my mol2 file. So I thought I'd use chimera to add charges & write, hopefully, a compatible mol2 file. I'm having problems with that as well. This is a pdb of the ligands:HETATM 8225 MG MG A 291 25.874 25.146 58.617 1.00 0.00 Mg2+ HETATM 8226 C4 FPS A 292 25.754 19.949 62.737 1.00 0.00 C HETATM 8227 C3 FPS A 292 26.088 21.273 63.475 1.00 0.00 C HETATM 8228 C2 FPS A 292 26.021 22.571 63.132 1.00 0.00 C HETATM 8229 C1 FPS A 292 25.656 23.447 61.998 1.00 0.00 C HETATM 8230 S1 FPS A 292 27.204 24.181 62.219 1.00 0.00 S HETATM 8231 P1 FPS A 292 27.928 23.762 60.771 1.00 0.00 P HETATM 8232 O1 FPS A 292 28.873 24.955 60.385 1.00 0.00 O HETATM 8233 P2 FPS A 292 28.554 26.180 59.405 1.00 0.00 P HETATM 8234 O2 FPS A 292 28.206 25.713 57.968 1.00 0.00 O HETATM 8235 O3 FPS A 292 27.331 26.943 59.830 1.00 0.00 O HETATM 8236 O4 FPS A 292 29.622 27.136 59.149 1.00 0.00 O HETATM 8237 O5 FPS A 292 26.862 23.528 59.683 1.00 0.00 O HETATM 8238 O6 FPS A 292 28.976 22.661 61.190 1.00 0.00 O HETATM 8239 C5 FPS A 292 26.754 21.192 64.778 1.00 0.00 C HETATM 8240 C6 FPS A 292 26.118 20.990 66.155 1.00 0.00 C HETATM 8241 C7 FPS A 292 27.084 20.015 66.840 1.00 0.00 C HETATM 8242 C8 FPS A 292 28.144 20.342 67.618 1.00 0.00 C HETATM 8243 C9 FPS A 292 28.586 21.777 67.991 1.00 0.00 C HETATM 8244 C10 FPS A 292 28.618 19.212 68.506 1.00 0.00 C HETATM 8245 C11 FPS A 292 27.622 19.162 69.634 1.00 0.00 C HETATM 8246 C12 FPS A 292 27.899 18.054 70.615 1.00 0.00 C HETATM 8247 C13 FPS A 292 28.127 18.187 71.942 1.00 0.00 C HETATM 8248 C14 FPS A 292 28.131 19.492 72.723 1.00 0.00 C HETATM 8249 C15 FPS A 292 28.358 16.835 72.549 1.00 0.00 C HETATM 8250 H4 FPS A 292 24.677 19.881 62.580 1.00 0.00 H HETATM 8251 H5 FPS A 292 26.263 19.931 61.773 1.00 0.00 H HETATM 8252 H1 FPS A 292 25.472 22.838 61.113 1.00 0.00 H HETATM 8253 H11 FPS A 292 24.694 24.092 62.300 1.00 0.00 H HETATM 8254 H14 FPS A 292 28.310 18.659 67.618 1.00 0.00 H HETATM 8255 H15 FPS A 292 29.626 18.910 68.790 1.00 0.00 H HETATM 8256 H141 FPS A 292 28.344 19.287 73.772 1.00 0.00 H HETATM 8257 H142 FPS A 292 28.897 20.155 72.320 1.00 0.00 H HETATM 8258 H143 FPS A 292 27.155 19.970 72.638 1.00 0.00 H HETATM 8259 H91 FPS A 292 29.470 21.732 68.628 1.00 0.00 H HETATM 8260 H92 FPS A 292 28.821 22.333 67.083 1.00 0.00 H HETATM 8261 H93 FPS A 292 27.779 22.279 68.525 1.00 0.00 H HETATM 8262 H7 FPS A 292 26.852 18.977 66.652 1.00 0.00 H HETATM 8263 H61 FPS A 292 26.054 21.948 66.670 1.00 0.00 H HETATM 8264 H62 FPS A 292 25.117 20.575 66.036 1.00 0.00 H HETATM 8265 H51 FPS A 292 27.451 20.354 64.779 1.00 0.00 H HETATM 8266 H52 FPS A 292 27.298 22.117 64.967 1.00 0.00 H HETATM 8267 H4 FPS A 292 26.087 19.103 63.338 1.00 0.00 H HETATM 8268 H12 FPS A 292 27.905 17.074 70.162 1.00 0.00 H HETATM 8269 H151 FPS A 292 28.547 16.946 73.646 1.00 0.00 H HETATM 8270 H152 FPS A 292 27.455 16.195 72.388 1.00 0.00 H HETATM 8271 H153 FPS A 292 29.246 16.355 72.064 1.00 0.00 H HETATM 8272 H111 FPS A 292 27.646 20.103 70.183 1.00 0.00 H HETATM 8273 H112 FPS A 292 26.622 19.003 69.230 1.00 0.00 H HETATM 8274 H2 FPS A 292 26.305 23.333 63.843 1.00 0.00 H HETATM 8348 O3 IPE A 586 21.257 22.023 59.139 1.00 0.00 O HETATM 8349 C1 IPE A 586 21.725 22.610 60.331 1.00 0.00 C HETATM 8350 C2 IPE A 586 21.891 21.539 61.401 1.00 0.00 C HETATM 8351 C3 IPE A 586 22.135 21.746 62.732 1.00 0.00 C HETATM 8352 C4 IPE A 586 22.476 23.125 63.351 1.00 0.00 C HETATM 8353 C5 IPE A 586 22.090 20.534 63.651 1.00 0.00 C HETATM 8354 P1 IPE A 586 22.541 22.279 58.101 1.00 0.00 P HETATM 8355 O1 IPE A 586 23.289 23.718 58.505 1.00 0.00 O HETATM 8356 O2 IPE A 586 23.635 21.031 58.224 1.00 0.00 O HETATM 8357 O7 IPE A 586 21.980 22.381 56.596 1.00 0.00 O HETATM 8358 P2 IPE A 586 22.517 20.944 55.933 1.00 0.00 P HETATM 8359 O4 IPE A 586 24.120 21.122 55.494 1.00 0.00 O HETATM 8360 O5 IPE A 586 22.398 19.740 57.082 1.00 0.00 O HETATM 8361 O6 IPE A 586 21.597 20.552 54.601 1.00 0.00 O HETATM 8362 H6 IPE A 586 20.970 20.939 61.359 1.00 0.00 H HETATM 8363 H7 IPE A 586 22.711 20.896 61.047 1.00 0.00 H HETATM 8364 H4 IPE A 586 22.660 23.213 64.432 1.00 0.00 H HETATM 8365 H5 IPE A 586 22.534 24.017 62.710 1.00 0.00 H HETATM 8366 H1 IPE A 586 21.090 20.076 63.606 1.00 0.00 H HETATM 8367 H2 IPE A 586 22.843 19.801 63.329 1.00 0.00 H HETATM 8368 H3 IPE A 586 22.303 20.848 64.684 1.00 0.00 H HETATM 8369 H11 IPE A 586 22.687 23.089 60.148 1.00 0.00 H HETATM 8370 H12 IPE A 586 21.008 23.356 60.675 1.00 0.00 H END When I try to add charges, chimera chews on it for a bit, then gives me a message that amber has stopped running, check the log file. When I click on the log file, the only message is that I've had a crash. In the older version of chimera I was running, I also tried this with only the IPE & got the same behavior. Are my compounds just too nonstandard? Thanks! Irene Newhouse