Re: [Apbs-users] apbs-pymol plugin
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Re: [Apbs-users] apbs-pymol plugin
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From: Nathan B. <sob...@ya...> - 2005-06-20 14:21:58
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Hi Joel -- This is a problem with chain IDs; they need to be removed from the PQR file prior to input to APBS. Thanks, Nathan --- Joel Tyndall <joe...@ot...> wrote: > Hi folks, > > I finally got around to installing apbs. I've tried to run it thru the > pymol plugin and I get an error. It seems to run ok but then can't read > in the map file (see below). any help would be welcome > > J > > set grid > > coarsedim is [111.56420230865479, 104.21170161962509, 79.228497600555414] > finedim is [85.626001358032227, 81.301000952720642, 66.604998588562012] > center is [13.830000877380371, 30.882500469684601, 25.5194993019104] > finegridpoints is [193, 193, 161] > radiobutton said to generate it Use PyMOL generated PQR and PyMOL > generated Hydrogens and termini so i am returning pymol-generated.pqr > radiobutton said to generate it Use PyMOL generated PQR and PyMOL > generated Hydrogens and termini so i am returning pymol-generated.pqr > WARNING: 124 atoms did not have formal charges assigned > WARNING: 264 atoms did not have properties assigned > > ---------------------------------------------------------------------- > APBS -- Adaptive Poisson-Boltzmann Solver > Version 0.3.2 > > ....... > > information about PMG and FEtk may be found at <http://www.FEtk.ORG>. > ---------------------------------------------------------------------- > > > This executable compiled on Nov 10 2004 at 11:39:22 > > Parsing input file pymol-generated.in... > parsePBE: Warning -- parsed deprecated "bcfl 1" statement > parsePBE: Please use "bcfl sdh" instead. > NOsh: Warning -- parsed deprecated statment "chgm 1". > NOsh: Please use "chgm spl2" instead! > parsePBE: Warning -- parsed deprecated "srfm 1" statement. > parsePBE: Please use "srfm smol" instead. > parsePBE: Warning -- parsed deprecated "calcenergy 0" statement. > parsePBE: Please use "calcenergy no" instead. > parsePBE: Warning -- parsed deprecated "calcforce 0" statement. > parsePBE: Please use "calcforce no" instead. > Parsed input file. > Got PQR paths for 1 molecules > Reading PQR-format atom data from pymol-generated.pqr. > Valist_readPDB: Unable to parse resSeq token (A) as int! > Valist_readPDB: Error while parsing residue name! > Valist_readPQR: Error parsing ATOM field! > Error while reading molecule from pymol-generated.pqr > Error reading molecules! > ObjectMapLoadDXFile-Error: Unable to open file! > > -- > Joel Tyndall, PhD > > Lecturer > National School of Pharmacy > University of Otago > PO Box 913 Dunedin > New Zealand > > Pukenga > Te Kura Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 913 Otepoti > Aotearoa > > Ph / Waea +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 > > > > ATOM 1 C ACE A 23 24.288 17.826 14.313 0.000 0.000 > ATOM 2 O ACE A 23 24.917 18.906 14.298 0.000 0.000 > ATOM 3 C ACE A 23 22.864 17.702 13.793 0.000 0.000 > ATOM 4 H ACE A 23 22.472 16.715 14.037 0.000 0.000 > ATOM 5 H ACE A 23 22.858 17.839 12.712 0.000 0.000 > ATOM 6 H ACE A 23 22.240 18.465 14.258 0.000 0.000 > ATOM 7 N GLY A 24 24.767 16.666 14.754 -0.416 1.824 > ATOM 8 CA GLY A 24 26.114 16.416 15.194 -0.025 1.908 > ATOM 9 C GLY A 24 26.119 16.275 16.728 0.597 1.908 > ATOM 10 O GLY A 24 26.108 15.189 17.316 -0.568 1.661 > ATOM 11 HA3 GLY A 24 26.756 17.246 14.900 0.070 1.387 > ATOM 12 H GLY A 24 24.125 15.887 14.783 0.272 0.600 > ATOM 13 HA GLY A 24 26.488 15.499 14.738 0.070 1.387 > ATOM 14 N SER A 25 26.082 17.456 17.330 -0.416 1.824 > ATOM 15 CA SER A 25 26.050 17.650 18.768 -0.025 1.908 > ATOM 16 C SER A 25 25.103 18.838 19.026 0.597 1.908 > ATOM 17 O SER A 25 24.852 19.618 18.088 -0.568 1.661 > ATOM 18 CB SER A 25 27.481 18.052 19.186 0.212 1.908 > ATOM 19 OG SER A 25 27.632 19.358 18.606 -0.655 1.721 > ATOM 20 HG SER A 25 27.486 20.027 19.279 0.428 0.000 > ATOM 21 H SER A 25 26.076 18.280 16.746 0.272 0.600 > ATOM 22 HA SER A 25 25.720 16.765 19.313 0.084 1.387 > ATOM 23 HB2 SER A 25 28.217 17.356 18.784 0.035 1.387 > ATOM 24 HB3 SER A 25 27.632 18.041 20.265 0.035 1.387 > ATOM 25 N ILE A 26 24.639 18.867 20.260 -0.416 1.824 > ATOM 26 CA ILE A 26 23.549 19.815 20.576 -0.060 1.908 > ATOM 27 C ILE A 26 24.058 21.261 20.462 0.597 1.908 > ATOM 28 O ILE A 26 23.209 22.114 20.153 -0.568 1.661 > ATOM 29 CB ILE A 26 22.962 19.478 21.981 0.130 1.908 > ATOM 30 CG1 ILE A 26 21.788 20.471 22.340 -0.043 1.908 > ATOM 31 CG2 ILE A 26 23.978 19.371 23.126 -0.320 1.908 > ATOM 32 CD1 ILE A 26 20.527 20.085 21.481 -0.066 1.908 > ATOM 33 HD13 ILE A 26 20.179 19.093 21.771 0.019 1.487 > ATOM 34 H ILE A 26 25.018 18.258 20.971 0.272 0.600 > ATOM 35 HA ILE A 26 22.737 19.717 19.856 0.087 1.387 > ATOM 36 HB ILE A 26 22.576 18.463 21.886 0.019 1.487 > ATOM 37 HG12 ILE A 26 22.089 21.494 22.114 0.024 1.487 > ATOM 38 HG23 ILE A 26 24.295 18.334 23.235 0.088 1.487 > ATOM 39 HD12 ILE A 26 20.793 20.083 20.424 0.019 1.487 > ATOM 40 HG13 ILE A 26 21.552 20.401 23.402 0.024 1.487 > ATOM 41 HG22 ILE A 26 23.518 19.710 24.054 0.088 1.487 > ATOM 42 HD11 ILE A 26 19.734 20.812 21.654 0.019 1.487 > ATOM 43 HG21 ILE A 26 24.844 19.994 22.902 0.088 1.487 > ATOM 44 N GLY A 27 25.346 21.441 20.740 -0.416 1.824 > ATOM 45 CA GLY A 27 25.967 22.810 20.689 -0.025 1.908 > ATOM 46 C GLY A 27 25.881 23.325 19.252 0.597 1.908 > ATOM 47 O GLY A 27 25.258 24.368 18.941 -0.568 1.661 > ATOM 48 HA3 GLY A 27 27.010 22.754 20.999 0.070 1.387 > ATOM 49 H GLY A 27 25.916 20.646 20.989 0.272 0.600 > ATOM 50 HA GLY A 27 25.439 23.486 21.361 0.070 1.387 > ATOM 51 N ALA A 28 26.464 22.566 18.365 -0.416 1.824 > ATOM 52 CA ALA A 28 26.464 22.821 16.913 0.034 1.908 > ATOM 53 C ALA A 28 25.054 22.924 16.353 0.597 1.908 > ATOM 54 O ALA A 28 24.728 23.841 15.561 -0.568 1.661 > ATOM 55 CB ALA A 28 27.204 21.691 16.230 -0.183 1.908 > ATOM 56 HB3 ALA A 28 27.330 21.925 15.173 0.060 1.487 > ATOM 57 H ALA A 28 26.950 21.745 18.697 0.272 0.600 > ATOM 58 HA ALA A 28 26.955 23.776 16.728 0.082 1.387 > ATOM 59 HB2 ALA A 28 26.634 20.768 16.333 0.060 1.487 > ATOM 60 HB1 ALA A 28 28.183 21.566 16.693 0.060 1.487 > ATOM 61 N ALA A 29 24.207 21.956 16.745 -0.416 1.824 > ATOM 62 CA ALA A 29 22.835 21.972 16.180 0.034 1.908 > ATOM 63 C ALA A 29 22.040 23.179 16.660 0.597 1.908 > ATOM 64 O ALA A 29 21.285 23.769 15.836 -0.568 1.661 > ATOM 65 CB ALA A 29 22.109 20.655 16.465 -0.183 1.908 > ATOM 66 HB3 ALA A 29 21.958 20.548 17.539 0.060 1.487 > ATOM 67 H ALA A 29 24.494 21.243 17.401 0.272 0.600 > ATOM 68 HA ALA A 29 22.923 22.068 15.098 0.082 1.387 > ATOM 69 HB2 ALA A 29 22.708 19.822 16.097 0.060 1.487 > ATOM 70 HB1 ALA A 29 21.142 20.657 15.961 0.060 1.487 > ATOM 71 N SER A 30 22.130 23.529 17.952 -0.416 1.824 > ATOM 72 CA SER A 30 21.294 24.711 18.383 -0.025 1.908 > ATOM 73 C SER A 30 21.772 26.016 17.762 0.597 1.908 > ATOM 74 O SER A 30 21.040 26.949 17.447 -0.568 1.661 > ATOM 75 CB SER A 30 21.212 24.798 19.907 0.212 1.908 > ATOM 76 OG SER A 30 22.528 25.088 20.378 -0.655 1.721 > ATOM 77 HG SER A 30 22.868 24.333 20.864 0.428 0.000 > ATOM 78 H SER A 30 22.723 23.030 18.600 0.272 0.600 > ATOM 79 HA SER A 30 20.284 24.548 18.006 0.084 1.387 > ATOM 80 HB2 SER A 30 20.866 23.850 20.319 0.035 1.387 > ATOM 81 HB3 SER A 30 20.509 25.571 20.216 0.035 1.387 > ATOM 82 N MET A 31 23.053 26.083 17.540 -0.416 1.824 > ATOM 83 CA MET A 31 23.689 27.330 17.000 -0.024 1.908 > ATOM 84 C MET A 31 23.345 27.428 15.549 0.597 1.908 > ATOM 85 O MET A 31 22.943 28.475 15.021 -0.568 1.661 > ATOM 86 CB MET A 31 25.217 27.123 17.193 0.034 1.908 > ATOM 87 CG MET A 31 25.435 27.429 18.679 0.002 1.908 > ATOM 88 SD MET A 31 26.027 29.166 18.675 -0.274 2.000 > ATOM 89 CE MET A 31 27.784 28.762 18.463 -0.054 1.908 > ATOM 90 HE3 MET A 31 28.115 29.086 17.476 0.068 1.387 > ATOM 91 H MET A 31 23.631 25.278 17.735 0.272 0.600 > ATOM 92 HA MET A 31 23.355 28.242 17.494 0.088 1.387 > ATOM 93 HB2 MET A 31 25.786 27.809 16.566 0.024 1.487 > ATOM 94 HG2 MET A 31 26.183 26.763 19.109 0.044 1.387 > ATOM 95 HE2 MET A 31 27.924 27.685 18.559 0.068 1.387 > ATOM 96 HB3 MET A 31 25.548 26.123 16.913 0.024 1.487 > ATOM 97 HG3 MET A 31 24.535 27.288 19.278 0.044 1.387 > ATOM 98 HE1 MET A 31 28.369 29.273 19.228 0.068 1.387 > ATOM 99 N GLU A 32 23.528 26.285 14.864 0.000 0.000 > ATOM 100 C GLU A 32 23.054 26.425 13.417 0.000 0.000 > ATOM 101 C GLU A 32 21.595 26.777 13.352 0.000 0.000 > ATOM 102 O GLU A 32 21.176 27.692 12.606 0.000 0.000 > ATOM 103 C GLU A 32 23.341 25.159 12.644 0.000 0.000 > ATOM 104 C GLU A 32 24.793 24.655 12.660 0.000 0.000 > ATOM 105 H GLU A 32 25.138 24.507 11.637 0.000 0.000 > ATOM 106 H GLU A 32 23.927 25.443 15.255 0.000 0.000 > ATOM 107 H GLU A 32 23.608 27.243 12.957 0.000 0.000 > ATOM 108 H GLU A 32 23.063 25.336 11.605 0.000 0.000 > ATOM 109 H GLU A 32 24.844 23.710 13.201 0.000 0.000 > ATOM 110 H GLU A 32 22.763 24.382 13.143 0.000 0.000 > ATOM 111 H GLU A 32 25.427 25.391 13.154 0.000 0.000 > ATOM 112 N PHE A 33 20.752 26.053 14.131 -0.416 1.824 > ATOM 113 CA PHE A 33 19.304 26.419 14.182 -0.002 1.908 > ATOM 114 C PHE A 33 19.109 27.896 14.516 0.597 1.908 > ATOM 115 O PHE A 33 18.325 28.634 13.848 -0.568 1.661 > ATOM 116 CB PHE A 33 18.492 25.486 15.111 -0.034 1.908 > ATOM 117 CG PHE A 33 17.001 25.776 15.157 0.012 1.908 > ATOM 118 CD1 PHE A 33 16.208 25.535 14.025 -0.126 1.908 > ATOM 119 CD2 PHE A 33 16.394 26.279 16.298 -0.126 1.908 > ATOM 120 CE1 PHE A 33 14.857 25.777 14.038 -0.170 1.908 > ATOM 121 CE2 PHE A 33 15.024 26.522 16.361 -0.170 1.908 > ATOM 122 CZ PHE A 33 14.255 26.274 15.213 -0.107 1.908 > ATOM 123 HZ PHE A 33 13.182 26.467 15.230 0.130 1.459 > ATOM 124 H PHE A 33 21.100 25.274 14.671 0.272 0.600 > ATOM 125 HA PHE A 33 18.901 26.267 13.181 0.098 1.387 > ATOM 126 HB2 PHE A 33 18.889 25.583 16.122 0.030 1.487 > ATOM 127 HD1 PHE A 33 16.673 25.148 13.118 0.133 1.459 > ATOM 128 HD2 PHE A 33 17.008 26.491 17.173 0.133 1.459 > ATOM 129 HE1 PHE A 33 14.255 25.587 13.149 0.143 1.459 > ATOM 130 HE2 PHE A 33 14.562 26.894 17.276 0.143 1.459 > ATOM 131 HB3 PHE A 33 18.597 24.480 14.704 0.030 1.487 > ATOM 132 N CYS A 34 19.723 28.330 15.596 -0.416 1.824 > ATOM 133 CA CYS A 34 19.703 29.767 15.995 0.021 1.908 > ATOM 134 C CYS A 34 19.908 30.765 14.838 0.597 1.908 > ATOM 135 O CYS A 34 19.143 31.752 14.648 -0.568 1.661 > ATOM 136 CB CYS A 34 20.718 29.985 17.127 -0.123 1.908 > ATOM 137 SG CYS A 34 20.701 31.739 17.619 -0.312 2.000 > ATOM 138 HG CYS A 34 21.752 32.367 17.074 0.193 0.600 > ATOM 139 H CYS A 34 20.224 27.669 16.173 0.272 0.600 > ATOM 140 HA CYS A 34 18.694 29.985 16.346 0.112 1.387 > ATOM 141 HB2 CYS A 34 21.715 29.713 16.781 0.111 1.387 > ATOM 142 HB3 CYS A 34 20.452 29.363 17.982 0.111 1.387 > ATOM 143 N PHE A 35 20.901 30.534 13.997 -0.416 1.824 > ATOM 144 CA PHE A 35 21.305 31.507 12.929 -0.002 1.908 > ATOM 145 C PHE A 35 20.390 31.361 11.743 0.597 1.908 > ATOM 146 O PHE A 35 20.027 32.391 11.201 -0.568 1.661 > ATOM 147 CB PHE A 35 22.813 31.268 12.588 -0.034 1.908 > ATOM 148 CG PHE A 35 23.662 31.873 13.708 0.012 1.908 > ATOM 149 CD1 PHE A 35 23.510 33.247 13.990 -0.126 1.908 > ATOM 150 CD2 PHE A 35 24.558 31.066 14.411 -0.126 1.908 > ATOM 151 CE1 PHE A 35 24.241 33.795 15.049 -0.170 1.908 > ATOM 152 CE2 PHE A 35 25.318 31.616 15.473 -0.170 1.908 > ATOM 153 CZ PHE A 35 25.118 32.979 15.758 -0.107 1.908 > ATOM 154 HZ PHE A 35 25.681 33.421 16.580 0.130 1.459 > ATOM 155 H PHE A 35 21.410 29.665 14.077 0.272 0.600 > ATOM 156 HA PHE A 35 21.205 32.539 13.267 0.098 1.387 > ATOM 157 HB2 PHE A 35 23.057 31.747 11.640 0.030 1.487 > ATOM 158 HD1 PHE A 35 22.838 33.867 13.396 0.133 1.459 > ATOM 159 HD2 PHE A 35 24.673 30.016 14.144 0.133 1.459 > ATOM 160 HE1 PHE A 35 24.126 34.846 15.315 0.143 1.459 > ATOM 161 HE2 PHE A 35 26.024 31.012 16.042 0.143 1.459 > ATOM 162 HB3 PHE A 35 23.013 30.200 12.501 0.030 1.487 > ATOM 163 N ASP A 36 19.885 30.157 11.532 -0.516 1.824 > ATOM 164 CA ASP A 36 18.776 30.042 10.532 0.038 1.908 > ATOM 165 C ASP A 36 17.586 30.883 10.914 0.537 1.908 > ATOM 166 O ASP A 36 16.975 31.568 10.060 -0.582 1.661 > ATOM 167 CB ASP A 36 18.408 28.591 10.259 -0.030 1.908 > ATOM 168 CG ASP A 36 19.407 27.873 9.364 0.799 1.908 > ATOM 169 OD1 ASP A 36 20.298 28.500 8.781 -0.801 1.661 > ATOM 170 OD2 ASP A 36 19.262 26.643 9.326 -0.801 1.661 > ATOM 171 HB2 ASP A 36 17.431 28.566 9.777 -0.012 1.487 > ATOM 172 H ASP A 36 20.233 29.348 12.025 0.294 0.600 > ATOM 173 HA ASP A 36 19.146 30.447 9.590 0.088 1.387 > ATOM 174 HB3 ASP A 36 18.406 28.074 11.218 -0.012 1.487 > ATOM 175 N VAL A 37 17.163 30.722 12.174 -0.416 1.824 > ATOM 176 CA VAL A 37 15.980 31.547 12.617 -0.087 1.908 > ATOM 177 C VAL A 37 16.291 33.048 12.486 0.597 1.908 > ATOM 178 O VAL A 37 15.433 33.885 12.098 -0.568 1.661 > ATOM 179 CB VAL A 37 15.557 31.095 14.043 0.299 1.908 > ATOM 180 CG1 VAL A 37 14.559 32.074 14.645 -0.319 1.908 > ATOM 181 CG2 VAL A 37 14.944 29.674 14.023 -0.319 1.908 > ATOM 182 HG23 VAL A 37 14.798 29.326 15.046 0.079 1.487 > ATOM 183 H VAL A 37 17.617 30.075 12.802 0.272 0.600 > ATOM 184 HA VAL A 37 15.120 31.381 11.968 0.097 1.387 > ATOM 185 HB VAL A 37 16.456 31.077 14.659 -0.030 1.487 > ATOM 186 HG13 VAL A 37 14.364 32.878 13.935 0.079 1.487 > ATOM 187 HG22 VAL A 37 15.617 28.995 13.500 0.079 1.487 > ATOM 188 HG12 VAL A 37 14.969 32.492 15.564 0.079 1.487 > ATOM 189 HG21 VAL A 37 13.984 29.700 13.508 0.079 1.487 > ATOM 190 HG11 VAL A 37 13.628 31.552 14.867 0.079 1.487 > ATOM 191 N PHE A 38 17.483 33.411 12.929 -0.416 1.824 > ATOM 192 CA PHE A 38 17.911 34.841 12.926 -0.002 1.908 > ATOM 193 C PHE A 38 17.806 35.454 11.516 0.597 1.908 > ATOM 194 O PHE A 38 17.258 36.547 11.372 -0.568 1.661 > ATOM 195 CB PHE A 38 19.318 34.985 13.540 -0.034 1.908 > ATOM 196 CG PHE A 38 19.672 36.438 13.773 0.012 1.908 > ATOM 197 CD1 PHE A 38 18.970 37.189 14.703 -0.126 1.908 > ATOM 198 CD2 PHE A 38 20.695 37.035 12.992 -0.126 1.908 > ATOM 199 CE1 PHE A 38 19.276 38.541 14.938 -0.170 1.908 > ATOM 200 CE2 PHE A 38 21.001 38.397 13.223 -0.170 1.908 > ATOM 201 CZ PHE A 38 20.318 39.142 14.194 -0.107 1.908 > === message truncated ===> # > # Note that most of the comments here were taken from sample > # input files that came with APBS. You can find APBS at > # http://agave.wustl.edu/apbs/ > # Note that APBS is GPL'd code. > # > read > mol pqr pymol-generated.pqr # read molecule 1 > end > elec > mg-auto > dime 193 193 161 # number of find grid points > # calculated by psize.py > cglen 111.564202 104.211702 79.228498 # coarse mesh lengths (A) > fglen 85.626001 81.301001 66.604999 # fine mesh lengths (A) > # calculated by psize.py > cgcent 13.830001 30.882500 25.519499 # (could also give (x,y,z) form > psize.py) #known center > fgcent 13.830001 30.882500 25.519499 # (could also give (x,y,z) form > psize.py) #known center > npbe # solve the full nonlinear PBE with npbe > #lpbe # solve the linear PBE with lpbe > bcfl 1 # Boundary condition flag > # 0 => Zero > # 1 => Single DH sphere > # 2 => Multiple DH spheres > # 4 => Focusing > # > #ion 1 0.000 2.0 # Counterion declaration: > ion 1 0.000000 2.000000 # Counterion declaration: > ion -1 0.000000 2.000000 # ion <charge> <conc (M)> <radius> > ion 2 0.000000 2.000000 # ion <charge> <conc (M)> <radius> > ion -2 0.000000 2.000000 # ion <charge> <conc (M)> <radius> > pdie 20.000000 # Solute dielectric > sdie 80.000000 # Solvent dielectric > chgm 1 # Charge disc method > # 0 is linear splines > # 1 is cubic b-splines > mol 1 # which molecule to use > srfm 1 # Surface calculation method > # 0 => Mol surface for epsilon; > # inflated VdW for kappa; no > # smoothing > # 1 => As 0 with harmoic average > # smoothing > # 2 => Cubic spline > srad 1.400000 # Solvent radius (1.4 for water) > swin 0.3 # Surface cubic spline window .. default 0.3 > temp 310.000000 # System temperature (298.15 default) > gamma 0.105 # Surface tension parameter for apolar forces (in > kJ/mol/A^2) > # only used for force calculations, so we don't care, > but > # it's always required, and 0.105 is the default > calcenergy 0 # Energy I/O to stdout > # 0 => don't write out energy > # 1 => write out total energy > # 2 => write out total energy and all > # components > calcforce 0 # Atomic forces I/O (to stdout) > # 0 => don't write out forces > # 1 => write out net forces on molecule > # 2 => write out atom-level forces > write pot dx pymol-generated # What to write .. this says write the > potential in dx > # format to a file. > end > quit > > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu |