Re: [Apbs-users] Bug in APBS version under VMD 1.8.4 windows version?
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Re: [Apbs-users] Bug in APBS version under VMD 1.8.4 windows version?
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From: Todd D. <to...@cc...> - 2006-01-18 19:31:32
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Hi James - Apparently that was the one step I forgot - in APBS 0.4.0 we've added a new SDENS keyword, so the plugin authors needed to add that to their respective code in order to get things to work again. We just heard from John Stone (who works on the VMD project) that he will b= e releasing a test VMD build today which (among other things) both fixes the apbs_fd problem and accounts for the SDENS keyword. This will be available from: http://www.ks.uiuc.edu/Research/vmd/alpha/ I think the current beta VMD build (1.8.4b6) also resolves these issues, so you'll probably want to either download the current beta or wait for the ne= w build. That should hopefully do it! Todd On 1/18/06, James Ianni <ji...@sa...> wrote: > > > Thanks for the really quick reply! > Okay, I tried 1,3 and 4. I'm having trouble trying to do 2 (mainly > obtaining the software). > I'm getting the same error: > > ------------------ > This executable compiled on Dec 14 2005 at 13:18:08 > > Parsing input file apbs.in... > PBEparm_check: SDENS not set! > NOsh: MG parameters not set correctly! > Error while parsing input file. > ---------------- > > Here is my .in file followed by the 1PTR.pqr file (VMD generated, I haven= t > added H's to this protein yet): > > read > mol pqr /tmp/1PTR.pqr > end > elec > mg-auto > dime 129 129 129 > cglen 34.8914988042 36.7124977112 40.5314970017 > cgcent mol 1 > fglen 23.2609992028 24.4749984741 27.0209980011 > fgcent mol 1 > mol 1 > lpbe > bcfl sdh > srfm smol > chgm spl2 > ion 1 0.150 2.0 > ion -1 0.150 2.0 > pdie 1.0 > sdie 78.54 > srad 1.4 > swin 0.3 > temp 298.15 > gamma 0.105 > calcenergy no > calcforce no > write pot dx pot > end > quit > ATOM 1 N HIS 231 20.224 17.337 46.492 0.000 1.400 > ATOM 2 CA HIS 231 19.782 18.342 45.533 0.000 1.500 > ATOM 3 C HIS 231 18.797 19.350 46.100 0.000 1.500 > ATOM 4 O HIS 231 17.952 19.045 46.941 0.000 1.300 > ATOM 5 CB HIS 231 19.137 17.701 44.319 0.000 1.500 > ATOM 6 CG HIS 231 20.052 16.769 43.538 0.000 1.500 > ATOM 7 ND1 HIS 231 20.994 17.148 42.673 0.000 1.400 > ATOM 8 CD2 HIS 231 19.830 15.428 43.492 0.000 1.500 > ATOM 9 CE1 HIS 231 21.344 16.037 42.071 0.000 1.500 > ATOM 10 NE2 HIS 231 20.653 15.028 42.560 0.000 1.400 > ATOM 11 N ARG 232 18.932 20.565 45.608 0.000 1.400 > ATOM 12 CA ARG 232 18.068 21.665 45.970 0.000 1.500 > ATOM 13 C ARG 232 17.296 22.047 44.698 0.000 1.500 > ATOM 14 O ARG 232 17.687 22.979 43.986 0.000 1.300 > ATOM 15 CB ARG 232 19.033 22.718 46.473 0.000 1.500 > ATOM 16 CG ARG 232 18.499 23.782 47.383 0.000 1.500 > ATOM 17 CD ARG 232 19.608 24.122 48.385 0.000 1.500 > ATOM 18 NE ARG 232 20.803 24.718 47.803 0.000 1.400 > ATOM 19 CZ ARG 232 20.855 25.993 47.405 0.000 1.500 > ATOM 20 NH1 ARG 232 19.813 26.825 47.477 0.000 1.400 > ATOM 21 NH2 ARG 232 21.986 26.449 46.896 0.000 1.400 > ATOM 22 N PHE 233 16.273 21.286 44.315 0.000 1.400 > ATOM 23 CA PHE 233 15.507 21.526 43.103 0.000 1.500 > ATOM 24 C PHE 233 14.471 22.597 43.233 0.000 1.500 > ATOM 25 O PHE 233 13.583 22.514 44.086 0.000 1.300 > ATOM 26 CB PHE 233 14.776 20.307 42.666 0.000 1.500 > ATOM 27 CG PHE 233 15.646 19.265 42.018 0.000 1.500 > ATOM 28 CD1 PHE 233 16.259 19.557 40.796 0.000 1.500 > ATOM 29 CD2 PHE 233 15.795 18.018 42.618 0.000 1.500 > ATOM 30 CE1 PHE 233 17.027 18.598 40.161 0.000 1.500 > ATOM 31 CE2 PHE 233 16.565 17.060 41.966 0.000 1.500 > ATOM 32 CZ PHE 233 17.176 17.350 40.743 0.000 1.500 > ATOM 33 N LYS 234 14.547 23.604 42.377 0.000 1.400 > ATOM 34 CA LYS 234 13.549 24.651 42.373 0.000 1.500 > ATOM 35 C LYS 234 13.070 24.793 40.938 0.000 1.500 > ATOM 36 O LYS 234 13.790 24.491 39.973 0.000 1.300 > ATOM 37 CB LYS 234 14.152 25.970 42.868 0.000 1.500 > ATOM 38 N VAL 235 11.784 25.148 40.820 0.000 1.400 > ATOM 39 CA VAL 235 11.153 25.242 39.519 0.000 1.500 > ATOM 40 C VAL 235 11.881 26.293 38.707 0.000 1.500 > ATOM 41 O VAL 235 12.306 27.333 39.223 0.000 1.300 > ATOM 42 CB VAL 235 9.637 25.591 39.678 0.000 1.500 > ATOM 43 CG1 VAL 235 9.403 27.021 40.137 0.000 1.500 > ATOM 44 CG2 VAL 235 8.976 25.432 38.332 0.000 1.500 > ATOM 45 N TYR 236 12.008 26.017 37.422 0.000 1.400 > ATOM 46 CA TYR 236 12.733 26.927 36.575 0.000 1.500 > ATOM 47 C TYR 236 11.889 27.059 35.332 0.000 1.500 > ATOM 48 O TYR 236 11.186 26.121 34.942 0.000 1.300 > ATOM 49 CB TYR 236 14.117 26.294 36.332 0.000 1.500 > ATOM 50 CG TYR 236 15.179 27.239 35.790 0.000 1.500 > ATOM 51 CD1 TYR 236 15.297 27.359 34.407 0.000 1.500 > ATOM 52 CD2 TYR 236 16.027 27.965 36.643 0.000 1.500 > ATOM 53 CE1 TYR 236 16.256 28.191 33.855 0.000 1.500 > ATOM 54 CE2 TYR 236 16.990 28.810 36.089 0.000 1.500 > ATOM 55 CZ TYR 236 17.085 28.901 34.704 0.000 1.500 > ATOM 56 OH TYR 236 18.026 29.689 34.100 0.000 1.300 > ATOM 57 N ASN 237 11.945 28.242 34.743 0.000 1.400 > ATOM 58 CA ASN 237 11.273 28.535 33.494 0.000 1.500 > ATOM 59 C ASN 237 12.414 28.592 32.504 0.000 1.500 > ATOM 60 O ASN 237 13.322 29.415 32.632 0.000 1.300 > ATOM 61 CB ASN 237 10.584 29.891 33.514 0.000 1.500 > ATOM 62 CG ASN 237 9.634 30.055 34.687 0.000 1.500 > ATOM 63 OD1 ASN 237 8.972 29.104 35.100 0.000 1.300 > ATOM 64 ND2 ASN 237 9.533 31.226 35.284 0.000 1.400 > ATOM 65 N TYR 238 12.408 27.708 31.520 0.000 1.400 > ATOM 66 CA TYR 238 13.514 27.562 30.593 0.000 1.500 > ATOM 67 C TYR 238 13.267 28.365 29.349 0.000 1.500 > ATOM 68 O TYR 238 12.140 28.535 28.873 0.000 1.300 > ATOM 69 CB TYR 238 13.721 26.098 30.218 0.000 1.500 > ATOM 70 CG TYR 238 14.121 25.257 31.420 0.000 1.500 > ATOM 71 CD1 TYR 238 13.147 24.823 32.313 0.000 1.500 > ATOM 72 CD2 TYR 238 15.457 24.930 31.633 0.000 1.500 > ATOM 73 CE1 TYR 238 13.502 24.060 33.421 0.000 1.500 > ATOM 74 CE2 TYR 238 15.821 24.161 32.738 0.000 1.500 > ATOM 75 CZ TYR 238 14.837 23.732 33.631 0.000 1.500 > ATOM 76 OH TYR 238 15.176 22.972 34.736 0.000 1.300 > ATOM 77 N MET 239 14.404 28.879 28.901 0.000 1.400 > ATOM 78 CA MET 239 14.450 29.777 27.773 0.000 1.500 > ATOM 79 C MET 239 14.789 29.121 26.453 0.000 1.500 > ATOM 80 O MET 239 14.583 29.726 25.407 0.000 1.300 > ATOM 81 CB MET 239 15.445 30.899 28.062 0.000 1.500 > ATOM 82 CG MET 239 15.013 31.742 29.244 0.000 1.500 > ATOM 83 SD MET 239 13.271 32.211 29.179 0.000 1.900 > ATOM 84 CE MET 239 13.159 33.120 27.671 0.000 1.500 > ATOM 85 N SER 240 15.309 27.905 26.452 0.000 1.400 > ATOM 86 CA SER 240 15.551 27.180 25.219 0.000 1.500 > ATOM 87 C SER 240 15.292 25.720 25.542 0.000 1.500 > ATOM 88 O SER 240 15.263 25.381 26.732 0.000 1.300 > ATOM 89 CB SER 240 16.981 27.410 24.775 0.000 1.500 > ATOM 90 OG SER 240 17.904 27.052 25.790 0.000 1.300 > ATOM 91 N PRO 241 15.029 24.829 24.591 0.000 1.400 > ATOM 92 CA PRO 241 14.718 23.441 24.875 0.000 1.500 > ATOM 93 C PRO 241 15.807 22.711 25.638 0.000 1.500 > ATOM 94 O PRO 241 16.958 22.581 25.196 0.000 1.300 > ATOM 95 CB PRO 241 14.420 22.836 23.527 0.000 1.500 > ATOM 96 CG PRO 241 15.061 23.781 22.534 0.000 1.500 > ATOM 97 CD PRO 241 14.877 25.133 23.180 0.000 1.500 > ATOM 98 N THR 242 15.375 22.288 26.821 0.000 1.400 > ATOM 99 CA THR 242 16.166 21.618 27.829 0.000 1.500 > ATOM 100 C THR 242 15.522 20.258 28.065 0.000 1.500 > ATOM 101 O THR 242 14.301 20.077 28.001 0.000 1.300 > ATOM 102 CB THR 242 16.145 22.449 29.106 0.000 1.500 > ATOM 103 OG1 THR 242 16.409 23.780 28.696 0.000 1.300 > ATOM 104 CG2 THR 242 17.195 22.049 30.140 0.000 1.500 > ATOM 105 N PHE 243 16.356 19.264 28.299 0.000 1.400 > ATOM 106 CA PHE 243 15.894 17.927 28.540 0.000 1.500 > ATOM 107 C PHE 243 16.108 17.598 29.983 0.000 1.500 > ATOM 108 O PHE 243 16.869 18.203 30.744 0.000 1.300 > ATOM 109 CB PHE 243 16.647 16.933 27.705 0.000 1.500 > ATOM 110 CG PHE 243 16.345 17.184 26.242 0.000 1.500 > ATOM 111 CD1 PHE 243 16.940 18.265 25.573 0.000 1.500 > ATOM 112 CD2 PHE 243 15.476 16.322 25.575 0.000 1.500 > ATOM 113 CE1 PHE 243 16.659 18.481 24.233 0.000 1.500 > ATOM 114 CE2 PHE 243 15.203 16.544 24.230 0.000 1.500 > ATOM 115 CZ PHE 243 15.790 17.617 23.559 0.000 1.500 > ATOM 116 N CYS 244 15.352 16.610 30.362 0.000 1.400 > ATOM 117 CA CYS 244 15.459 16.121 31.705 0.000 1.500 > ATOM 118 C CYS 244 16.713 15.259 31.814 0.000 1.500 > ATOM 119 O CYS 244 16.813 14.183 31.197 0.000 1.300 > ATOM 120 CB CYS 244 14.208 15.352 31.945 0.000 1.500 > ATOM 121 SG CYS 244 14.068 14.451 33.484 0.000 1.900 > ATOM 122 N ASP 245 17.578 15.650 32.732 0.000 1.400 > ATOM 123 CA ASP 245 18.801 14.913 32.989 0.000 1.500 > ATOM 124 C ASP 245 18.582 13.565 33.591 0.000 1.500 > ATOM 125 O ASP 245 19.516 12.769 33.702 0.000 1.300 > ATOM 126 CB ASP 245 19.711 15.743 33.892 0.000 1.500 > ATOM 127 CG ASP 245 20.259 16.974 33.185 0.000 1.500 > ATOM 128 OD1 ASP 245 20.441 16.955 31.963 0.000 1.300 > ATOM 129 OD2 ASP 245 20.496 17.965 33.857 0.000 1.300 > ATOM 130 N HIS 246 17.360 13.297 34.035 0.000 1.400 > ATOM 131 CA HIS 246 17.067 11.959 34.506 0.000 1.500 > ATOM 132 C HIS 246 16.522 11.042 33.416 0.000 1.500 > ATOM 133 O HIS 246 16.985 9.917 33.248 0.000 1.300 > ATOM 134 CB HIS 246 16.064 12.021 35.684 0.000 1.500 > ATOM 135 CG HIS 246 15.615 10.633 36.121 0.000 1.500 > ATOM 136 ND1 HIS 246 16.292 9.731 36.800 0.000 1.400 > ATOM 137 CD2 HIS 246 14.423 10.057 35.763 0.000 1.500 > ATOM 138 CE1 HIS 246 15.592 8.645 36.858 0.000 1.500 > ATOM 139 NE2 HIS 246 14.467 8.852 36.228 0.000 1.400 > ATOM 140 N CYS 247 15.525 11.493 32.644 0.000 1.400 > ATOM 141 CA CYS 247 14.875 10.524 31.746 0.000 1.500 > ATOM 142 C CYS 247 15.145 10.794 30.280 0.000 1.500 > ATOM 143 O CYS 247 14.751 10.005 29.440 0.000 1.300 > ATOM 144 CB CYS 247 13.346 10.491 31.926 0.000 1.500 > ATOM 145 SG CYS 247 12.443 11.926 31.279 0.000 1.900 > ATOM 146 N GLY 248 15.753 11.913 29.925 0.000 1.400 > ATOM 147 CA GLY 248 16.021 12.163 28.528 0.000 1.500 > ATOM 148 C GLY 248 14.926 12.899 27.788 0.000 1.500 > ATOM 149 O GLY 248 15.276 13.444 26.744 0.000 1.300 > ATOM 150 N SER 249 13.644 12.961 28.186 0.000 1.400 > ATOM 151 CA SER 249 12.701 13.753 27.407 0.000 1.500 > ATOM 152 C SER 249 12.712 15.226 27.734 0.000 1.500 > ATOM 153 O SER 249 13.086 15.643 28.846 0.000 1.300 > ATOM 154 CB SER 249 11.259 13.257 27.583 0.000 1.500 > ATOM 155 OG SER 249 11.128 11.877 27.312 0.000 1.300 > ATOM 156 N LEU 250 12.284 15.968 26.704 0.000 1.400 > ATOM 157 CA LEU 250 12.136 17.405 26.778 0.000 1.500 > ATOM 158 C LEU 250 11.324 17.864 27.983 0.000 1.500 > ATOM 159 O LEU 250 10.327 17.243 28.368 0.000 1.300 > ATOM 160 CB LEU 250 11.462 17.891 25.497 0.000 1.500 > ATOM 161 CG LEU 250 11.289 19.386 25.224 0.000 1.500 > ATOM 162 CD1 LEU 250 12.648 20.047 24.942 0.000 1.500 > ATOM 163 CD2 LEU 250 10.364 19.548 24.040 0.000 1.500 > ATOM 164 N LEU 251 11.748 18.958 28.587 0.000 1.400 > ATOM 165 CA LEU 251 11.037 19.601 29.654 0.000 1.500 > ATOM 166 C LEU 251 9.978 20.429 28.942 0.000 1.500 > ATOM 167 O LEU 251 10.204 21.564 28.522 0.000 1.300 > ATOM 168 CB LEU 251 11.986 20.483 30.446 0.000 1.500 > ATOM 169 CG LEU 251 13.103 19.757 31.199 0.000 1.500 > ATOM 170 CD1 LEU 251 13.871 20.756 32.035 0.000 1.500 > ATOM 171 CD2 LEU 251 12.523 18.645 32.058 0.000 1.500 > ATOM 172 N TRP 252 8.792 19.850 28.795 0.000 1.400 > ATOM 173 CA TRP 252 7.707 20.427 28.010 0.000 1.500 > ATOM 174 C TRP 252 7.129 21.699 28.556 0.000 1.500 > ATOM 175 O TRP 252 7.104 21.878 29.777 0.000 1.300 > ATOM 176 CB TRP 252 6.531 19.468 27.898 0.000 1.500 > ATOM 177 CG TRP 252 6.914 18.045 27.580 0.000 1.500 > ATOM 178 CD1 TRP 252 7.267 17.638 26.317 0.000 1.500 > ATOM 179 CD2 TRP 252 6.949 17.049 28.504 0.000 1.500 > ATOM 180 NE1 TRP 252 7.530 16.358 26.451 0.000 1.400 > ATOM 181 CE2 TRP 252 7.362 15.967 27.723 0.000 1.500 > ATOM 182 CE3 TRP 252 6.701 16.899 29.855 0.000 1.500 > ATOM 183 CZ2 TRP 252 7.535 14.713 28.289 0.000 1.500 > ATOM 184 CZ3 TRP 252 6.872 15.641 30.423 0.000 1.500 > ATOM 185 CH2 TRP 252 7.287 14.563 29.650 0.000 1.500 > ATOM 186 N GLY 253 6.630 22.573 27.691 0.000 1.400 > ATOM 187 CA GLY 253 5.872 23.708 28.192 0.000 1.500 > ATOM 188 C GLY 253 6.514 25.050 27.950 0.000 1.500 > ATOM 189 O GLY 253 7.671 25.149 27.558 0.000 1.300 > ATOM 190 N LEU 254 5.752 26.094 28.200 0.000 1.400 > ATOM 191 CA LEU 254 6.221 27.442 28.002 0.000 1.500 > ATOM 192 C LEU 254 6.910 27.988 29.231 0.000 1.500 > ATOM 193 O LEU 254 7.856 28.778 29.131 0.000 1.300 > ATOM 194 CB LEU 254 5.038 28.326 27.627 0.000 1.500 > ATOM 195 CG LEU 254 4.370 28.029 26.269 0.000 1.500 > ATOM 196 CD1 LEU 254 3.032 28.747 26.236 0.000 1.500 > ATOM 197 CD2 LEU 254 5.262 28.457 25.107 0.000 1.500 > ATOM 198 N VAL 255 6.446 27.573 30.411 0.000 1.400 > ATOM 199 CA VAL 255 6.992 28.047 31.676 0.000 1.500 > ATOM 200 C VAL 255 6.993 26.869 32.618 0.000 1.500 > ATOM 201 O VAL 255 6.280 25.886 32.398 0.000 1.300 > ATOM 202 CB VAL 255 6.137 29.162 32.332 0.000 1.500 > ATOM 203 CG1 VAL 255 6.184 30.429 31.487 0.000 1.500 > ATOM 204 CG2 VAL 255 4.691 28.699 32.460 0.000 1.500 > ATOM 205 N LYS 256 7.788 26.961 33.666 0.000 1.400 > ATOM 206 CA LYS 256 7.834 25.976 34.739 0.000 1.500 > ATOM 207 C LYS 256 7.980 24.534 34.276 0.000 1.500 > ATOM 208 O LYS 256 7.526 23.573 34.919 0.000 1.300 > ATOM 209 CB LYS 256 6.566 26.157 35.603 0.000 1.500 > ATOM 210 CG LYS 256 6.457 27.586 36.134 0.000 1.500 > ATOM 211 CD LYS 256 5.237 27.929 36.979 0.000 1.500 > ATOM 212 CE LYS 256 3.895 27.654 36.327 0.000 1.500 > ATOM 213 NZ LYS 256 3.503 26.272 36.556 0.000 1.400 > ATOM 214 N GLN 257 8.726 24.370 33.191 0.000 1.400 > ATOM 215 CA GLN 257 8.908 23.083 32.548 0.000 1.500 > ATOM 216 C GLN 257 9.548 22.008 33.404 0.000 1.500 > ATOM 217 O GLN 257 9.376 20.804 33.151 0.000 1.300 > ATOM 218 CB GLN 257 9.759 23.218 31.309 0.000 1.500 > ATOM 219 CG GLN 257 9.221 24.153 30.250 0.000 1.500 > ATOM 220 CD GLN 257 9.766 25.568 30.335 0.000 1.500 > ATOM 221 OE1 GLN 257 10.059 26.081 31.413 0.000 1.300 > ATOM 222 NE2 GLN 257 9.922 26.268 29.229 0.000 1.400 > ATOM 223 N GLY 258 10.300 22.401 34.425 0.000 1.400 > ATOM 224 CA GLY 258 10.965 21.430 35.265 0.000 1.500 > ATOM 225 C GLY 258 11.647 22.097 36.427 0.000 1.500 > ATOM 226 O GLY 258 11.398 23.265 36.711 0.000 1.300 > ATOM 227 N LEU 259 12.522 21.379 37.097 0.000 1.400 > ATOM 228 CA LEU 259 13.166 21.853 38.306 0.000 1.500 > ATOM 229 C LEU 259 14.668 21.759 38.070 0.000 1.500 > ATOM 230 O LEU 259 15.153 20.742 37.568 0.000 1.300 > ATOM 231 CB LEU 259 12.749 20.957 39.484 0.000 1.500 > ATOM 232 CG LEU 259 11.254 20.819 39.799 0.000 1.500 > ATOM 233 CD1 LEU 259 10.936 19.368 40.048 0.000 1.500 > ATOM 234 CD2 LEU 259 10.885 21.645 41.008 0.000 1.500 > ATOM 235 N LYS 260 15.404 22.807 38.384 0.000 1.400 > ATOM 236 CA LYS 260 16.845 22.789 38.263 0.000 1.500 > ATOM 237 C LYS 260 17.441 22.844 39.673 0.000 1.500 > ATOM 238 O LYS 260 17.042 23.661 40.528 0.000 1.300 > ATOM 239 CB LYS 260 17.296 23.988 37.447 0.000 1.500 > ATOM 240 CG LYS 260 18.811 24.109 37.323 0.000 1.500 > ATOM 241 CD LYS 260 19.101 25.389 36.603 0.000 1.500 > ATOM 242 CE LYS 260 18.995 25.057 35.150 0.000 1.500 > ATOM 243 NZ LYS 260 18.625 26.239 34.424 0.000 1.400 > ATOM 244 N CYS 261 18.380 21.939 39.951 0.000 1.400 > ATOM 245 CA CYS 261 19.114 21.926 41.197 0.000 1.500 > ATOM 246 C CYS 261 20.022 23.139 41.278 0.000 1.500 > ATOM 247 O CYS 261 20.945 23.296 40.473 0.000 1.300 > ATOM 248 CB CYS 261 19.994 20.710 41.326 0.000 1.500 > ATOM 249 SG CYS 261 20.979 20.713 42.850 0.000 1.900 > ATOM 250 N GLU 262 19.789 23.917 42.329 0.000 1.400 > ATOM 251 CA GLU 262 20.554 25.107 42.641 0.000 1.500 > ATOM 252 C GLU 262 22.032 24.859 42.875 0.000 1.500 > ATOM 253 O GLU 262 22.830 25.756 42.685 0.000 1.300 > ATOM 254 CB GLU 262 19.990 25.757 43.865 0.000 1.500 > ATOM 255 CG GLU 262 18.611 26.320 43.636 0.000 1.500 > ATOM 256 CD GLU 262 18.327 27.457 44.600 0.000 1.500 > ATOM 257 OE1 GLU 262 18.843 28.548 44.348 0.000 1.300 > ATOM 258 OE2 GLU 262 17.616 27.252 45.593 0.000 1.300 > ATOM 259 N ASP 263 22.412 23.671 43.333 0.000 1.400 > ATOM 260 CA ASP 263 23.817 23.380 43.539 0.000 1.500 > ATOM 261 C ASP 263 24.538 22.769 42.336 0.000 1.500 > ATOM 262 O ASP 263 25.642 23.171 42.011 0.000 1.300 > ATOM 263 CB ASP 263 23.956 22.447 44.747 0.000 1.500 > ATOM 264 CG ASP 263 23.310 22.984 46.013 0.000 1.500 > ATOM 265 OD1 ASP 263 23.511 24.154 46.323 0.000 1.300 > ATOM 266 OD2 ASP 263 22.599 22.231 46.683 0.000 1.300 > ATOM 267 N CYS 264 23.923 21.835 41.595 0.000 1.400 > ATOM 268 CA CYS 264 24.689 21.161 40.548 0.000 1.500 > ATOM 269 C CYS 264 24.131 21.426 39.158 0.000 1.500 > ATOM 270 O CYS 264 24.662 20.886 38.196 0.000 1.300 > ATOM 271 CB CYS 264 24.716 19.646 40.746 0.000 1.500 > ATOM 272 SG CYS 264 23.106 18.812 40.547 0.000 1.900 > ATOM 273 N GLY 265 23.017 22.164 39.000 0.000 1.400 > ATOM 274 CA GLY 265 22.441 22.388 37.684 0.000 1.500 > ATOM 275 C GLY 265 21.677 21.223 37.078 0.000 1.500 > ATOM 276 O GLY 265 21.312 21.317 35.916 0.000 1.300 > ATOM 277 N MET 266 21.498 20.081 37.739 0.000 1.400 > ATOM 278 CA MET 266 20.652 19.000 37.226 0.000 1.500 > ATOM 279 C MET 266 19.244 19.524 36.922 0.000 1.500 > ATOM 280 O MET 266 18.683 20.268 37.731 0.000 1.300 > ATOM 281 CB MET 266 20.554 17.876 38.251 0.000 1.500 > ATOM 282 CG MET 266 19.917 16.649 37.650 0.000 1.500 > ATOM 283 SD MET 266 19.741 15.252 38.760 0.000 1.900 > ATOM 284 CE MET 266 19.557 13.985 37.552 0.000 1.500 > ATOM 285 N ASN 267 18.666 19.130 35.798 0.000 1.400 > ATOM 286 CA ASN 267 17.367 19.617 35.348 0.000 1.500 > ATOM 287 C ASN 267 16.460 18.421 35.326 0.000 1.500 > ATOM 288 O ASN 267 16.826 17.408 34.705 0.000 1.300 > ATOM 289 CB ASN 267 17.378 20.135 33.937 0.000 1.500 > ATOM 290 CG ASN 267 18.299 21.316 33.746 0.000 1.500 > ATOM 291 OD1 ASN 267 18.244 22.287 34.479 0.000 1.300 > ATOM 292 ND2 ASN 267 19.212 21.298 32.795 0.000 1.400 > ATOM 293 N VAL 268 15.310 18.443 36.005 0.000 1.400 > ATOM 294 CA VAL 268 14.383 17.316 35.973 0.000 1.500 > ATOM 295 C VAL 268 12.950 17.772 35.736 0.000 1.500 > ATOM 296 O VAL 268 12.542 18.913 35.924 0.000 1.300 > ATOM 297 CB VAL 268 14.410 16.444 37.299 0.000 1.500 > ATOM 298 CG1 VAL 268 15.856 15.977 37.492 0.000 1.500 > ATOM 299 CG2 VAL 268 13.888 17.180 38.541 0.000 1.500 > ATOM 300 N HIS 269 12.164 16.789 35.323 0.000 1.400 > ATOM 301 CA HIS 269 10.744 16.996 35.077 0.000 1.500 > ATOM 302 C HIS 269 10.191 16.948 36.477 0.000 1.500 > ATOM 303 O HIS 269 10.696 16.156 37.281 0.000 1.300 > ATOM 304 CB HIS 269 10.011 15.852 34.375 0.000 1.500 > ATOM 305 CG HIS 269 10.207 15.701 32.877 0.000 1.500 > ATOM 306 ND1 HIS 269 10.851 14.693 32.317 0.000 1.400 > ATOM 307 CD2 HIS 269 9.744 16.579 31.951 0.000 1.500 > ATOM 308 CE1 HIS 269 10.794 14.933 31.026 0.000 1.500 > ATOM 309 NE2 HIS 269 10.142 16.046 30.824 0.000 1.400 > ATOM 310 N HIS 270 9.102 17.656 36.717 0.000 1.400 > ATOM 311 CA HIS 270 8.368 17.558 37.971 0.000 1.500 > ATOM 312 C HIS 270 8.122 16.102 38.341 0.000 1.500 > ATOM 313 O HIS 270 8.345 15.713 39.491 0.000 1.300 > ATOM 314 CB HIS 270 7.043 18.276 37.827 0.000 1.500 > ATOM 315 CG HIS 270 7.221 19.781 37.759 0.000 1.500 > ATOM 316 ND1 HIS 270 7.280 20.616 38.782 0.000 1.400 > ATOM 317 CD2 HIS 270 7.336 20.521 36.611 0.000 1.500 > ATOM 318 CE1 HIS 270 7.427 21.833 38.307 0.000 1.500 > ATOM 319 NE2 HIS 270 7.459 21.760 37.003 0.000 1.400 > ATOM 320 N LYS 271 7.757 15.254 37.366 0.000 1.400 > ATOM 321 CA LYS 271 7.519 13.833 37.599 0.000 1.500 > ATOM 322 C LYS 271 8.757 13.010 37.849 0.000 1.500 > ATOM 323 O LYS 271 8.665 11.914 38.394 0.000 1.300 > ATOM 324 CB LYS 271 6.804 13.167 36.432 0.000 1.500 > ATOM 325 CG LYS 271 7.609 13.096 35.132 0.000 1.500 > ATOM 326 CD LYS 271 6.796 12.321 34.129 0.000 1.500 > ATOM 327 CE LYS 271 7.341 12.528 32.749 0.000 1.500 > ATOM 328 NZ LYS 271 6.459 11.830 31.834 0.000 1.400 > ATOM 329 N CYS 272 9.914 13.510 37.432 0.000 1.400 > ATOM 330 CA CYS 272 11.153 12.766 37.599 0.000 1.500 > ATOM 331 C CYS 272 11.912 13.134 38.868 0.000 1.500 > ATOM 332 O CYS 272 12.840 12.419 39.238 0.000 1.300 > ATOM 333 CB CYS 272 12.062 12.987 36.407 0.000 1.500 > ATOM 334 SG CYS 272 11.345 12.207 34.943 0.000 1.900 > ATOM 335 N ARG 273 11.564 14.228 39.531 0.000 1.400 > ATOM 336 CA ARG 273 12.240 14.624 40.743 0.000 1.500 > ATOM 337 C ARG 273 12.196 13.463 41.725 0.000 1.500 > ATOM 338 O ARG 273 13.260 13.045 42.162 0.000 1.300 > ATOM 339 CB ARG 273 11.552 15.850 41.325 0.000 1.500 > ATOM 340 N GLU 274 11.066 12.778 41.959 0.000 1.400 > ATOM 341 CA GLU 274 11.029 11.660 42.909 0.000 1.500 > ATOM 342 C GLU 274 11.882 10.443 42.520 0.000 1.500 > ATOM 343 O GLU 274 12.143 9.542 43.325 0.000 1.300 > ATOM 344 CB GLU 274 9.591 11.168 43.094 0.000 1.500 > ATOM 345 N LYS 275 12.309 10.422 41.260 0.000 1.400 > ATOM 346 CA LYS 275 13.055 9.333 40.700 0.000 1.500 > ATOM 347 C LYS 275 14.564 9.576 40.749 0.000 1.500 > ATOM 348 O LYS 275 15.342 8.690 40.390 0.000 1.300 > ATOM 349 CB LYS 275 12.604 9.159 39.281 0.000 1.500 > ATOM 350 CG LYS 275 11.148 8.815 38.986 0.000 1.500 > ATOM 351 CD LYS 275 11.011 8.995 37.465 0.000 1.500 > ATOM 352 CE LYS 275 9.616 8.754 36.889 0.000 1.500 > ATOM 353 NZ LYS 275 9.598 9.054 35.462 0.000 1.400 > ATOM 354 N VAL 276 15.031 10.753 41.136 0.000 1.400 > ATOM 355 CA VAL 276 16.451 11.057 41.122 0.000 1.500 > ATOM 356 C VAL 276 17.091 10.615 42.435 0.000 1.500 > ATOM 357 O VAL 276 16.449 10.643 43.485 0.000 1.300 > ATOM 358 CB VAL 276 16.586 12.590 40.871 0.000 1.500 > ATOM 359 CG1 VAL 276 18.018 13.068 40.934 0.000 1.500 > ATOM 360 CG2 VAL 276 16.152 12.880 39.455 0.000 1.500 > ATOM 361 N ALA 277 18.349 10.176 42.441 0.000 1.400 > ATOM 362 CA ALA 277 19.034 9.825 43.680 0.000 1.500 > ATOM 363 C ALA 277 19.295 11.081 44.456 0.000 1.500 > ATOM 364 O ALA 277 19.484 12.163 43.889 0.000 1.300 > ATOM 365 CB ALA 277 20.392 9.212 43.472 0.000 1.500 > ATOM 366 N ASN 278 19.352 10.947 45.767 0.000 1.400 > ATOM 367 CA ASN 278 19.533 12.140 46.550 0.000 1.500 > ATOM 368 C ASN 278 20.870 12.832 46.538 0.000 1.500 > ATOM 369 O ASN 278 20.932 14.052 46.775 0.000 1.300 > ATOM 370 CB ASN 278 19.163 11.847 47.970 0.000 1.500 > ATOM 371 CG ASN 278 17.707 12.228 48.030 0.000 1.500 > ATOM 372 OD1 ASN 278 16.832 11.401 47.783 0.000 1.300 > ATOM 373 ND2 ASN 278 17.399 13.498 48.266 0.000 1.400 > ATOM 374 N LEU 279 21.928 12.094 46.221 0.000 1.400 > ATOM 375 CA LEU 279 23.248 12.680 46.296 0.000 1.500 > ATOM 376 C LEU 279 23.533 13.640 45.168 0.000 1.500 > ATOM 377 O LEU 279 23.347 13.349 43.995 0.000 1.300 > ATOM 378 CB LEU 279 24.268 11.546 46.338 0.000 1.500 > ATOM 379 CG LEU 279 25.721 11.786 46.760 0.000 1.500 > ATOM 380 CD1 LEU 279 25.819 12.780 47.906 0.000 1.500 > ATOM 381 CD2 LEU 279 26.293 10.458 47.200 0.000 1.500 > ATOM 382 N CYS 280 23.894 14.841 45.583 0.000 1.400 > ATOM 383 CA CYS 280 24.283 15.936 44.734 0.000 1.500 > ATOM 384 C CYS 280 25.781 16.090 44.952 0.000 1.500 > ATOM 385 O CYS 280 26.221 16.276 46.084 0.000 1.300 > ATOM 386 CB CYS 280 23.567 17.187 45.167 0.000 1.500 > ATOM 387 SG CYS 280 23.903 18.679 44.211 0.000 1.900 > ATOM 388 C1 PRB 3 10.006 23.859 22.583 0.000 1.500 > ATOM 389 C2 PRB 3 9.089 22.889 22.944 0.000 1.500 > ATOM 390 C3 PRB 3 8.773 23.057 24.276 0.000 1.500 > ATOM 391 O3 PRB 3 7.906 22.393 24.869 0.000 1.300 > ATOM 392 C4 PRB 3 9.456 24.274 24.872 0.000 1.500 > ATOM 393 O4 PRB 3 8.414 25.238 25.031 0.000 1.300 > ATOM 394 C5 PRB 3 10.134 23.934 26.222 0.000 1.500 > ATOM 395 C6 PRB 3 11.376 24.688 26.598 0.000 1.500 > ATOM 396 C7 PRB 3 11.695 25.936 26.067 0.000 1.500 > ATOM 397 C8 PRB 3 10.824 26.691 25.082 0.000 1.500 > ATOM 398 C9 PRB 3 10.821 26.183 23.597 0.000 1.500 > ATOM 399 O9 PRB 3 12.128 26.253 23.040 0.000 1.300 > ATOM 400 C10 PRB 3 10.544 24.583 23.796 0.000 1.500 > ATOM 401 C11 PRB 3 9.795 27.092 22.796 0.000 1.500 > ATOM 402 C12 PRB 3 10.330 28.536 22.726 0.000 1.500 > ATOM 403 O12 PRB 3 9.289 29.473 22.462 0.000 1.300 > ATOM 404 C13 PRB 3 11.024 29.055 24.004 0.000 1.500 > ATOM 405 C14 PRB 3 11.195 28.204 25.304 0.000 1.500 > ATOM 406 C15 PRB 3 10.431 29.462 25.395 0.000 1.500 > ATOM 407 C16 PRB 3 8.968 29.179 25.814 0.000 1.500 > ATOM 408 C17 PRB 3 11.008 30.670 26.154 0.000 1.500 > ATOM 409 C18 PRB 3 9.460 26.699 21.364 0.000 1.500 > ATOM 410 C19 PRB 3 8.520 21.842 22.024 0.000 1.500 > ATOM 411 C20 PRB 3 12.272 24.147 27.625 0.000 1.500 > ATOM 412 O20 PRB 3 12.543 22.751 27.509 0.000 1.300 > ATOM 413 OA1 PRB 3 12.040 30.019 23.705 0.000 1.300 > ATOM 414 CA1 PRB 3 13.110 29.782 22.769 0.000 1.500 > ATOM 415 OA2 PRB 3 13.387 28.621 22.424 0.000 1.300 > ATOM 416 CA2 PRB 3 13.899 30.940 22.171 0.000 1.500 > ATOM 417 ZN ZN 1 22.187 18.804 42.656 0.000 1.500 > ATOM 418 ZN ZN 2 12.105 13.302 33.098 0.000 1.500 > > > _______________________________________________________________ > Dr. James C. Ianni, MSc., Ph.D. > Department of Chemistry, > University of Pennsylvania, mailbox #254 > 231 South 34th Street, Philadelphia, PA 19104, USA > email: ji...@sa...; > tel.: 001 215-573-4249 (lab) > 001 215-573-6741 (office) > > -----Original Message----- > *From:* apb...@li... [mailto: > apb...@li...]*On Behalf Of *Todd Dolinsky > *Sent:* Wednesday, January 18, 2006 1:51 PM > *To:* ji...@sa... > *Cc:* apb...@li... > *Subject:* Re: [Apbs-users] Bug in APBS version under VMD 1.8.4 windows > version? > > Hi James - > > We've seen this error before, although we're still not sure what the exac= t > cause is - it looks to be a VMD error. I do have a couple of suggestions > for you: > > 1. Since it looks like you're running Windows, you might want to try jus= t > running APBS from the command line without VMD. > > 2. Assuming that works, make sure that you're using a PQR file instead o= f > a PDB file - while I believe that VMD can convert from one to the other, = if > we're trying to isolate the problem it'd be useful to start with a PQR > file. You can use pdb2pqr ( http://pdb2pqr.sourceforge.net) to do so. > > 3. Copy your PQR file and the executable to C:/ (or a subdirectory > without a space). This might resolve conflicts that could arise from spa= ces > in the file names, particularly when calling APBS. > > 4. First load your molecule into VMD, then open the APBS electrostatics > pane, and edit the settings to point to the correct APBS location. You ma= y > also want to set the working directory to the same directory, as I don't > think VMD can write to the /tmp directory in Windows. > > Hopefully this works! We've seen issues with spaces in the filenames wit= h > other Windows visualization programs, so that might be the key problem > here. I believe the VMD people are aware of this issue, so hopefully it > will be resolved soon. > > Please let me know how it goes! > > Todd > > On 1/18/06, James Ianni <ji...@sa...> wrote: > > > > > > All, > > > > I get the following error while running the > > latest greatest APBS version under VMD 1.8.4 windows version: > > > > > > Main console display active (Tcl8.4.1 / Tk8.4.1) > > apbsrun: using VMD radii > > apbsrun: using pqrplugin for /tmp/1PTR.pqr > > apbsrun: error running C:/Program Files/APBS/apbs.exe > > apbsrun: error occurred while running APBS: > > can't read "apbs_fd": no such variable > > (George Orr) 1 % > > > > > > Is there a fix for the current version of APBS or VMD > > to correct this? > > > > -James > > _______________________________________________________________ > > Dr. James C. Ianni, MSc., Ph.D. > > Department of Chemistry, > > University of Pennsylvania, mailbox #254 > > 231 South 34th Street, Philadelphia, PA 19104, USA > > email: ji...@sa...; > > tel.: 001 215-573-4249 (lab) > > 001 215-573-6741 (office) > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > > files > > for problems? Stop! Download the new AJAX search engine that makes > > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat= =3D121642 > > _______________________________________________ > > apbs-users mailing list > > apb...@li... > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > |
