Re: [Apbs-users] problem generating .dx file
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Re: [Apbs-users] problem generating .dx file
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From: Nathan B. <ba...@cc...> - 2007-08-19 23:06:00
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Hi All -- I'm pretty sure there's a pane in the APBS PyMOL interface that allows you to specify the path for writing the APBS-related files. Thanks, Nathan On 8/19/07, David Gohara <sd...@ma...> wrote: > Hi all, > > Actially I think pymol writes to the directory that it was started > from. At least on unix systems. I think. You may be able to set this > in the interface, though. > > Dave > > Sent from my iPhone > > On Aug 19, 2007, at 9:30 AM, Nathan Baker <ba...@cc...> wrote: > > > Hi Sarah -- > > > > This calculation worked for me. However, APBS wrote the DX file to a > > single file in the current directory with a filename of the path you > > were trying to write to (e.g., "D:\tmp\..."). Did you write this > > APBS input file by hand? I think the default behavior of the PyMOL > > APBS plugin is to write to the specified temporary directory. I'd > > try to take advantage of this default behavior -- perhaps the strange > > filename/path problems I noticed are part of the problem you're > > experiencing. > > > > Thanks, > > > > Nathan > > > > On Aug 16, 2007, at 12:10 PM, Sarah Kennedy wrote: > > > >> > >> Hello > >> I'm trying to run APBS with the pymol plugin. I have the latest > >> version of both programs. I am getting the same error that many > >> people have mentioned in the email archives. > >> > >> ObjectMapLoadDXFile-Error: Unable to open file! > >> > >> I've checked to maker sure that I don't have spaces in my > >> filenames. I've attached the files that should be useful for you to > >> help me. I would like to generate the electrostatic potential of > >> the pdb and view it with pymol. > >> Thanks so much! > >> Sarah > >> REMARK 1 PQR file generated by PDB2PQR (Version 1.2.1) > >> REMARK 1 > >> REMARK 1 Forcefield Used: amber > >> REMARK 1 > >> REMARK 5 WARNING: Unable to debump PRO A 42 > >> REMARK 5 WARNING: Unable to debump PRO A 259 > >> REMARK 5 > >> REMARK 6 Total charge on this protein: -8.0000 e > >> REMARK 6 > >> ATOM 1 N LYS 22 -8.909 -49.749 14.380 0.0966 1.8240 > >> ATOM 2 CA LYS 22 -7.524 -50.037 13.885 -0.0015 1.9080 > >> ATOM 3 CB LYS 22 -7.558 -50.882 12.614 0.0212 1.9080 > >> ATOM 4 CG LYS 22 -7.751 -52.399 12.786 -0.0048 1.9080 > >> ATOM 5 CD LYS 22 -7.479 -53.076 11.427 -0.0608 1.9080 > >> ATOM 6 CE LYS 22 -7.470 -54.595 11.518 -0.0181 1.9080 > >> ATOM 7 NZ LYS 22 -6.763 -55.137 10.325 -0.3764 1.8240 > >> ATOM 8 C LYS 22 -6.765 -48.753 13.566 0.7214 1.9080 > >> ATOM 9 O LYS 22 -5.519 -48.699 13.680 -0.6013 1.6612 > >> ATOM 10 HZ2 LYS 22 -5.778 -55.129 10.492 0.3382 0.6000 > >> ATOM 11 HA LYS 22 -7.037 -50.540 14.607 0.1180 1.1000 > >> ATOM 12 HD3 LYS 22 -6.590 -52.768 11.096 0.0633 1.4870 > >> ATOM 13 HD2 LYS 22 -8.194 -52.796 10.790 0.0633 1.4870 > >> ATOM 14 HE2 LYS 22 -6.989 -54.868 12.339 0.1171 1.1000 > >> ATOM 15 HE3 LYS 22 -8.403 -54.925 11.526 0.1171 1.1000 > >> ATOM 16 H2 LYS 22 -9.416 -49.287 13.658 0.2165 0.6000 > >> ATOM 17 H3 LYS 22 -9.350 -50.611 14.614 0.2165 0.6000 > >> ATOM 18 HG2 LYS 22 -7.102 -52.734 13.443 0.0121 1.4870 > >> ATOM 19 HG3 LYS 22 -8.679 -52.579 13.050 0.0121 1.4870 > >> ATOM 20 HZ1 LYS 22 -7.067 -56.074 10.158 0.3382 0.6000 > >> ATOM 21 HZ3 LYS 22 -6.973 -54.570 9.530 0.3382 0.6000 > >> ATOM 22 H LYS 22 -8.845 -49.165 15.184 0.2165 0.6000 > >> ATOM 23 HB3 LYS 22 -6.690 -50.740 12.116 0.0283 1.4870 > >> ATOM 24 HB2 LYS 22 -8.309 -50.545 12.029 0.0283 1.4870 > >> ATOM 25 N THR 23 -7.507 -47.737 13.119 -0.4157 1.8240 > >> ATOM 26 CA THR 23 -6.933 -46.398 12.963 -0.0389 1.9080 > >> ATOM 27 CB THR 23 -7.122 -45.790 11.515 0.3654 1.9080 > >> ATOM 28 OG1 THR 23 -6.479 -46.635 10.545 -0.6761 1.7210 > >> ATOM 29 CG2 THR 23 -6.564 -44.350 11.395 -0.2438 1.9080 > >> ATOM 30 C THR 23 -7.487 -45.505 14.075 0.5973 1.9080 > >> ATOM 31 O THR 23 -6.999 -44.397 14.283 -0.5679 1.6612 > >> ATOM 32 HG22 THR 23 -5.942 -44.176 12.157 0.0642 1.4870 > >> ATOM 33 H THR 23 -8.487 -47.971 12.901 0.2719 0.6000 > >> ATOM 34 HG21 THR 23 -6.074 -44.261 10.530 0.0642 1.4870 > >> ATOM 35 HB THR 23 -8.118 -45.765 11.315 0.0043 1.3870 > >> ATOM 36 HG23 THR 23 -7.323 -43.702 11.423 0.0642 1.4870 > >> ATOM 37 HA THR 23 -5.946 -46.460 13.072 0.1007 1.3870 > >> ATOM 38 HG1 THR 23 -6.282 -46.115 9.708 0.4102 0.0000 > >> ATOM 39 N ALA 24 -8.501 -46.017 14.782 -0.4157 1.8240 > >> ATOM 40 CA ALA 24 -9.028 -45.386 16.002 0.0337 1.9080 > >> ATOM 41 CB ALA 24 -10.362 -45.970 16.374 -0.1825 1.9080 > >> ATOM 42 C ALA 24 -8.034 -45.630 17.123 0.5973 1.9080 > >> ATOM 43 O ALA 24 -7.853 -44.790 18.010 -0.5679 1.6612 > >> ATOM 44 H ALA 24 -8.888 -46.906 14.393 0.2719 0.6000 > >> ATOM 45 HA ALA 24 -9.107 -44.407 15.844 0.0823 1.3870 > >> ATOM 46 HB1 ALA 24 -10.717 -46.525 15.618 0.0603 1.4870 > >> ATOM 47 HB3 ALA 24 -10.269 -46.550 17.187 0.0603 1.4870 > >> ATOM 48 HB2 ALA 24 -11.015 -45.236 16.572 0.0603 1.4870 > >> ATOM 49 N THR 25 -7.388 -46.789 17.024 -0.4157 1.8240 > >> ATOM 50 CA THR 25 -6.460 -47.307 17.997 -0.0389 1.9080 > >> ATOM 51 CB THR 25 -6.156 -48.811 17.710 0.3654 1.9080 > >> ATOM 52 OG1 THR 25 -7.385 -49.546 17.612 -0.6761 1.7210 > >> ATOM 53 CG2 THR 25 -5.243 -49.418 18.792 -0.2438 1.9080 > >> ATOM 54 C THR 25 -5.151 -46.510 17.969 0.5973 1.9080 > >> ATOM 55 O THR 25 -4.590 -46.180 19.021 -0.5679 1.6612 > >> ATOM 56 HG22 THR 25 -4.321 -49.531 18.422 0.0642 1.4870 > >> ATOM 57 H THR 25 -7.628 -47.317 16.129 0.2719 0.6000 > >> ATOM 58 HG21 THR 25 -5.215 -48.806 19.582 0.0642 1.4870 > >> ATOM 59 HB THR 25 -5.671 -48.875 16.817 0.0043 1.3870 > >> ATOM 60 HG23 THR 25 -5.605 -50.308 19.069 0.0642 1.4870 > >> ATOM 61 HA THR 25 -6.858 -47.213 18.916 0.1007 1.3870 > >> ATOM 62 HG1 THR 25 -7.529 -50.097 18.440 0.4102 0.0000 > >> ATOM 63 N ALA 26 -4.646 -46.220 16.774 -0.4157 1.8240 > >> ATOM 64 CA ALA 26 -3.391 -45.524 16.710 0.0337 1.9080 > >> ATOM 65 CB ALA 26 -2.710 -45.739 15.367 -0.1825 1.9080 > >> ATOM 66 C ALA 26 -3.655 -44.047 17.006 0.5973 1.9080 > >> ATOM 67 O ALA 26 -2.796 -43.367 17.586 -0.5679 1.6612 > >> ATOM 68 H ALA 26 -5.200 -46.520 15.971 0.2719 0.6000 > >> ATOM 69 HA ALA 26 -2.774 -45.877 17.410 0.0823 1.3870 > >> ATOM 70 HB1 ALA 26 -2.520 -44.854 14.943 0.0603 1.4870 > >> ATOM 71 HB3 ALA 26 -1.852 -46.234 15.502 0.0603 1.4870 > >> ATOM 72 HB2 ALA 26 -3.309 -46.271 14.769 0.0603 1.4870 > >> ATOM 73 N ARG 27 -4.856 -43.589 16.653 -0.3479 1.8240 > >> ATOM 74 CA ARG 27 -5.276 -42.217 16.849 -0.2637 1.9080 > >> ATOM 75 CB ARG 27 -6.572 -41.904 16.079 -0.0007 1.9080 > >> ATOM 76 CG ARG 27 -6.880 -40.397 16.008 0.0390 1.9080 > >> ATOM 77 CD ARG 27 -8.358 -40.081 15.909 0.0486 1.9080 > >> ATOM 78 NE ARG 27 -8.624 -38.646 15.791 -0.5295 1.8240 > >> ATOM 79 CZ ARG 27 -8.815 -37.812 16.826 0.8076 1.9080 > >> ATOM 80 NH1 ARG 27 -8.767 -38.279 18.076 -0.8627 1.8240 > >> ATOM 81 NH2 ARG 27 -9.043 -36.500 16.630 -0.8627 1.8240 > >> ATOM 82 C ARG 27 -5.512 -41.947 18.324 0.7341 1.9080 > >> ATOM 83 O ARG 27 -5.226 -40.858 18.817 -0.5894 1.6612 > >> ATOM 84 HG3 ARG 27 -6.419 -40.012 15.203 0.0285 1.4870 > >> ATOM 85 HA ARG 27 -4.551 -41.601 16.521 0.1560 1.3870 > >> ATOM 86 HE ARG 27 -8.668 -38.250 14.864 0.3456 0.6000 > >> ATOM 87 HD3 ARG 27 -8.807 -40.430 16.732 0.0687 1.3870 > >> ATOM 88 HD2 ARG 27 -8.725 -40.548 15.105 0.0687 1.3870 > >> ATOM 89 HG2 ARG 27 -6.515 -39.954 16.832 0.0285 1.4870 > >> ATOM 90 HH22 ARG 27 -9.199 -35.906 17.390 0.4478 0.6000 > >> ATOM 91 HH21 ARG 27 -9.048 -36.145 15.690 0.4478 0.6000 > >> ATOM 92 HH12 ARG 27 -8.931 -37.645 18.838 0.4478 0.6000 > >> ATOM 93 HH11 ARG 27 -8.571 -39.236 18.247 0.4478 0.6000 > >> ATOM 94 H ARG 27 -5.474 -44.320 16.216 0.2747 0.6000 > >> ATOM 95 HB3 ARG 27 -7.325 -42.345 16.542 0.0327 1.4870 > >> ATOM 96 HB2 ARG 27 -6.473 -42.237 15.154 0.0327 1.4870 > >> ATOM 97 N ALA 28 -6.066 -42.938 19.011 -0.4157 1.8240 > >> ATOM 98 CA ALA 28 -6.426 -42.814 20.409 0.0337 1.9080 > >> ATOM 99 CB ALA 28 -7.188 -44.043 20.863 -0.1825 1.9080 > >> ATOM 100 C ALA 28 -5.163 -42.612 21.225 0.5973 1.9080 > >> ATOM 101 O ALA 28 -5.056 -41.652 21.969 -0.5679 1.6612 > >> ATOM 102 H ALA 28 -6.219 -43.812 18.455 0.2719 0.6000 > >> ATOM 103 HA ALA 28 -7.015 -42.014 20.526 0.0823 1.3870 > >> ATOM 104 HB1 ALA 28 -7.343 -44.651 20.083 0.0603 1.4870 > >> ATOM 105 HB3 ALA 28 -6.660 -44.529 21.560 0.0603 1.4870 > >> ATOM 106 HB2 ALA 28 -8.070 -43.770 21.249 0.0603 1.4870 > >> ATOM 107 N LYS 29 -4.201 -43.505 21.050 -0.3479 1.8240 > >> ATOM 108 CA LYS 29 -2.895 -43.393 21.680 -0.2400 1.9080 > >> ATOM 109 CB LYS 29 -1.961 -44.512 21.169 -0.0094 1.9080 > >> ATOM 110 CG LYS 29 -2.406 -45.922 21.620 0.0187 1.9080 > >> ATOM 111 CD LYS 29 -1.491 -47.065 21.143 -0.0479 1.9080 > >> ATOM 112 CE LYS 29 -2.049 -48.389 21.641 -0.0143 1.9080 > >> ATOM 113 NZ LYS 29 -1.254 -49.586 21.233 -0.3854 1.8240 > >> ATOM 114 C LYS 29 -2.272 -42.013 21.461 0.7341 1.9080 > >> ATOM 115 O LYS 29 -1.833 -41.377 22.408 -0.5894 1.6612 > >> ATOM 116 H LYS 29 -4.461 -44.300 20.418 0.2747 0.6000 > >> ATOM 117 HA LYS 29 -2.995 -43.544 22.675 0.1426 1.3870 > >> ATOM 118 HD3 LYS 29 -0.596 -46.930 21.525 0.0621 1.4870 > >> ATOM 119 HD2 LYS 29 -1.482 -47.069 20.160 0.0621 1.4870 > >> ATOM 120 HE2 LYS 29 -2.100 -48.361 22.653 0.1135 1.1000 > >> ATOM 121 HE3 LYS 29 -2.997 -48.494 21.296 0.1135 1.1000 > >> ATOM 122 HG2 LYS 29 -2.440 -45.939 22.628 0.0103 1.4870 > >> ATOM 123 HG3 LYS 29 -3.337 -46.090 21.272 0.0103 1.4870 > >> ATOM 124 HZ1 LYS 29 -0.471 -49.684 21.844 0.3400 0.6000 > >> ATOM 125 HB3 LYS 29 -1.053 -44.347 21.528 0.0362 1.4870 > >> ATOM 126 HZ3 LYS 29 -1.831 -50.399 21.291 0.3400 0.6000 > >> ATOM 127 HZ2 LYS 29 -0.936 -49.465 20.294 0.3400 0.6000 > >> ATOM 128 HB2 LYS 29 -1.963 -44.492 20.180 0.0362 1.4870 > >> ATOM 129 N VAL 30 -2.250 -41.540 20.219 -0.4157 1.8240 > >> ATOM 130 CA VAL 30 -1.568 -40.297 19.906 -0.0875 1.9080 > >> ATOM 131 CB VAL 30 -1.499 -40.082 18.377 0.2985 1.9080 > >> ATOM 132 CG1 VAL 30 -1.065 -38.671 18.027 -0.3192 1.9080 > >> ATOM 133 CG2 VAL 30 -0.534 -41.057 17.803 -0.3192 1.9080 > >> ATOM 134 C VAL 30 -2.173 -39.122 20.692 0.5973 1.9080 > >> ATOM 135 O VAL 30 -1.456 -38.329 21.291 -0.5679 1.6612 > >> ATOM 136 HG22 VAL 30 0.409 -40.767 17.992 0.0791 1.4870 > >> ATOM 137 H VAL 30 -2.746 -42.119 19.520 0.2719 0.6000 > >> ATOM 138 HG21 VAL 30 -0.677 -41.967 18.205 0.0791 1.4870 > >> ATOM 139 HG11 VAL 30 -0.100 -38.672 17.764 0.0791 1.4870 > >> ATOM 140 HG12 VAL 30 -1.616 -38.329 17.264 0.0791 1.4870 > >> ATOM 141 HG13 VAL 30 -1.191 -38.074 18.820 0.0791 1.4870 > >> ATOM 142 HB VAL 30 -2.423 -40.205 18.015 -0.0297 1.4870 > >> ATOM 143 HG23 VAL 30 -0.655 -41.123 16.808 0.0791 1.4870 > >> ATOM 144 HA VAL 30 -0.604 -40.382 20.183 0.0969 1.3870 > >> ATOM 145 N VAL 31 -3.499 -39.029 20.680 -0.4157 1.8240 > >> ATOM 146 CA VAL 31 -4.205 -38.062 21.512 -0.0875 1.9080 > >> ATOM 147 CB VAL 31 -5.719 -38.342 21.543 0.2985 1.9080 > >> ATOM 148 CG1 VAL 31 -6.342 -37.763 22.804 -0.3192 1.9080 > >> ATOM 149 CG2 VAL 31 -6.390 -37.778 20.300 -0.3192 1.9080 > >> ATOM 150 C VAL 31 -3.668 -38.064 22.940 0.5973 1.9080 > >> ATOM 151 O VAL 31 -3.026 -37.107 23.374 -0.5679 1.6612 > >> ATOM 152 HG22 VAL 31 -6.029 -36.865 20.113 0.0791 1.4870 > >> ATOM 153 H VAL 31 -3.977 -39.691 20.040 0.2719 0.6000 > >> ATOM 154 HG21 VAL 31 -6.205 -38.377 19.522 0.0791 1.4870 > >> ATOM 155 HG11 VAL 31 -7.331 -37.678 22.680 0.0791 1.4870 > >> ATOM 156 HG12 VAL 31 -6.155 -38.368 23.578 0.0791 1.4870 > >> ATOM 157 HG13 VAL 31 -5.951 -36.861 22.986 0.0791 1.4870 > >> ATOM 158 HB VAL 31 -5.844 -39.328 21.583 -0.0297 1.4870 > >> ATOM 159 HG23 VAL 31 -7.376 -37.722 20.451 0.0791 1.4870 > >> ATOM 160 HA VAL 31 -4.052 -37.144 21.125 0.0969 1.3870 > >> ATOM 161 N ASP 32 -3.935 -39.146 23.664 -0.5163 1.8240 > >> ATOM 162 CA ASP 32 -3.385 -39.327 25.003 0.0381 1.9080 > >> ATOM 163 CB ASP 32 -3.517 -40.787 25.442 -0.0303 1.9080 > >> ATOM 164 CG ASP 32 -4.919 -41.132 25.902 0.7994 1.9080 > >> ATOM 165 OD1 ASP 32 -5.779 -40.227 25.924 -0.8014 1.6612 > >> ATOM 166 OD2 ASP 32 -5.255 -42.281 26.261 -0.8014 1.6612 > >> ATOM 167 C ASP 32 -1.924 -38.893 25.062 0.5366 1.9080 > >> ATOM 168 O ASP 32 -1.530 -38.125 25.940 -0.5819 1.6612 > >> ATOM 169 H ASP 32 -4.557 -39.838 23.202 0.2936 0.6000 > >> ATOM 170 HB3 ASP 32 -2.886 -40.940 26.193 -0.0122 1.4870 > >> ATOM 171 HA ASP 32 -3.898 -38.719 25.621 0.0880 1.3870 > >> ATOM 172 HB2 ASP 32 -3.283 -41.362 24.667 -0.0122 1.4870 > >> ATOM 173 N TRP 33 -1.126 -39.390 24.123 -0.4157 1.8240 > >> ATOM 174 CA TRP 33 0.273 -38.993 24.018 -0.0275 1.9080 > >> ATOM 175 CB TRP 33 0.889 -39.538 22.728 -0.0050 1.9080 > >> ATOM 176 CG TRP 33 1.412 -40.935 22.858 -0.1415 1.9080 > >> ATOM 177 CD1 TRP 33 1.715 -41.595 24.014 -0.1638 1.9080 > >> ATOM 178 NE1 TRP 33 2.168 -42.861 23.733 -0.3418 1.8240 > >> ATOM 179 CE2 TRP 33 2.166 -43.042 22.374 0.1380 1.9080 > >> ATOM 180 CD2 TRP 33 1.695 -41.848 21.792 0.1243 1.9080 > >> ATOM 181 CE3 TRP 33 1.599 -41.779 20.398 -0.2387 1.9080 > >> ATOM 182 CZ3 TRP 33 1.968 -42.881 19.647 -0.1972 1.9080 > >> ATOM 183 CH2 TRP 33 2.431 -44.050 20.257 -0.1134 1.9080 > >> ATOM 184 CZ2 TRP 33 2.537 -44.151 21.616 -0.2601 1.9080 > >> ATOM 185 C TRP 33 0.421 -37.476 24.069 0.5973 1.9080 > >> ATOM 186 O TRP 33 1.247 -36.948 24.814 -0.5679 1.6612 > >> ATOM 187 HH2 TRP 33 2.688 -44.826 19.677 0.1417 1.4590 > >> ATOM 188 H TRP 33 -1.577 -40.073 23.483 0.2719 0.6000 > >> ATOM 189 HZ2 TRP 33 2.869 -44.985 22.068 0.1572 1.4590 > >> ATOM 190 HA TRP 33 0.761 -39.372 24.814 0.1123 1.3870 > >> ATOM 191 HE1 TRP 33 2.453 -43.541 24.407 0.3412 0.6000 > >> ATOM 192 HD1 TRP 33 1.622 -41.214 24.933 0.2062 1.4090 > >> ATOM 193 HE3 TRP 33 1.269 -40.951 19.948 0.1700 1.4590 > >> ATOM 194 HZ3 TRP 33 1.901 -42.835 18.653 0.1447 1.4590 > >> ATOM 195 HB3 TRP 33 1.652 -38.959 22.466 0.0339 1.4870 > >> ATOM 196 HB2 TRP 33 0.195 -39.546 22.019 0.0339 1.4870 > >> ATOM 197 N CYS 34 -0.384 -36.780 23.273 -0.4157 1.8240 > >> ATOM 198 CA CYS 34 -0.214 -35.346 23.077 0.0213 1.9080 > >> ATOM 199 CB CYS 34 -0.975 -34.881 21.834 -0.1231 1.9080 > >> ATOM 200 SG CYS 34 -0.169 -35.289 20.269 -0.3119 2.0000 > >> ATOM 201 C CYS 34 -0.679 -34.563 24.301 0.5973 1.9080 > >> ATOM 202 O CYS 34 -0.138 -33.502 24.613 -0.5679 1.6612 > >> ATOM 203 H CYS 34 -1.130 -37.337 22.812 0.2719 0.6000 > >> ATOM 204 HA CYS 34 0.767 -35.159 22.941 0.1124 1.3870 > >> ATOM 205 HB3 CYS 34 -1.075 -33.888 21.886 0 > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |