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|
#include "SimTKmolmodel.h"
#include "molmodel/internal/Pdb.h"
#include "SimTKcommon/Testing.h"
#include <sstream>
using namespace SimTK;
using namespace std;
void testProteinDihedrals() {
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DuMMForceFieldSubsystem dumm(system);
dumm.loadAmber99Parameters();
dumm.setGbsaGlobalScaleFactor(0);
dumm.setCoulombGlobalScaleFactor(0.0);
// vpfString is useful for ensuring cis-proline is set correctly
const char* vpfString = ""
"ATOM 66 N VAL A 14 1.688 -35.161 -4.509 1.00 10.89 N \n"
"ATOM 67 CA VAL A 14 2.776 -34.186 -4.429 1.00 9.30 C \n"
"ATOM 68 C VAL A 14 2.595 -33.225 -3.228 1.00 9.34 C \n"
"ATOM 69 O VAL A 14 1.506 -32.751 -2.953 1.00 9.03 O \n"
"ATOM 70 CB VAL A 14 2.855 -33.367 -5.740 1.00 11.74 C \n"
"ATOM 71 CG1 VAL A 14 3.946 -32.344 -5.654 1.00 12.55 C \n"
"ATOM 72 CG2 VAL A 14 3.097 -34.263 -6.929 1.00 14.44 C \n"
"ATOM 73 N PRO A 15 3.665 -32.948 -2.479 1.00 12.35 N \n"
"ATOM 74 CA PRO A 15 5.036 -33.449 -2.569 1.00 11.72 C \n"
"ATOM 75 C PRO A 15 5.379 -34.583 -1.577 1.00 13.93 C \n"
"ATOM 76 O PRO A 15 6.533 -34.744 -1.195 1.00 18.82 O \n"
"ATOM 77 CB PRO A 15 5.845 -32.202 -2.289 1.00 5.84 C \n"
"ATOM 78 CG PRO A 15 5.035 -31.517 -1.262 1.00 9.84 C \n"
"ATOM 79 CD PRO A 15 3.580 -31.870 -1.485 1.00 10.51 C \n"
"ATOM 80 N PHE A 16 4.402 -35.387 -1.186 1.00 8.41 N \n"
"ATOM 81 CA PHE A 16 4.666 -36.483 -0.284 1.00 8.06 C \n"
"ATOM 82 C PHE A 16 5.243 -37.743 -0.959 1.00 9.43 C \n"
"ATOM 83 O PHE A 16 6.202 -38.330 -0.453 1.00 8.42 O \n"
"ATOM 84 CB PHE A 16 3.396 -36.818 0.461 1.00 13.56 C \n"
"ATOM 85 CG PHE A 16 2.973 -35.765 1.423 1.00 12.62 C \n"
"ATOM 86 CD1 PHE A 16 2.157 -34.730 1.015 1.00 19.89 C \n"
"ATOM 87 CD2 PHE A 16 3.354 -35.829 2.747 1.00 13.73 C \n"
"ATOM 88 CE1 PHE A 16 1.727 -33.767 1.923 1.00 16.04 C \n"
"ATOM 89 CE2 PHE A 16 2.927 -34.885 3.645 1.00 13.91 C \n"
"ATOM 90 CZ PHE A 16 2.114 -33.853 3.232 1.00 14.41 C \n"
;
const char* gbpFrag1String = ""
"ATOM 1 N LEU A 5 9.888 -56.161 4.597 1.00 11.43 N \n"
"ATOM 2 CA LEU A 5 8.638 -55.368 4.770 1.00 15.74 C \n"
"ATOM 3 C LEU A 5 8.247 -54.783 3.426 1.00 15.40 C \n"
"ATOM 4 O LEU A 5 9.120 -54.406 2.670 1.00 16.47 O \n"
"ATOM 5 CB LEU A 5 8.870 -54.246 5.786 1.00 10.24 C \n"
"ATOM 6 CG LEU A 5 9.191 -54.738 7.194 1.00 11.95 C \n"
"ATOM 7 CD1 LEU A 5 9.455 -53.563 8.053 1.00 8.81 C \n"
"ATOM 8 CD2 LEU A 5 8.028 -55.526 7.782 1.00 15.35 C \n"
"ATOM 9 N VAL A 6 6.963 -54.862 3.079 1.00 16.79 N \n"
"ATOM 10 CA VAL A 6 6.398 -54.229 1.880 1.00 13.57 C \n"
"ATOM 11 C VAL A 6 5.624 -52.996 2.304 1.00 13.60 C \n"
"ATOM 12 O VAL A 6 4.613 -53.132 2.972 1.00 8.66 O \n"
"ATOM 13 CB VAL A 6 5.386 -55.148 1.199 1.00 15.73 C \n"
"ATOM 14 CG1 VAL A 6 4.937 -54.539 -0.110 1.00 12.94 C \n"
"ATOM 15 CG2 VAL A 6 5.982 -56.537 1.004 1.00 17.64 C \n"
"ATOM 16 N VAL A 7 6.094 -51.809 1.929 1.00 9.96 N \n"
"ATOM 17 CA VAL A 7 5.446 -50.564 2.320 1.00 9.01 C \n"
"ATOM 18 C VAL A 7 4.806 -49.930 1.098 1.00 6.87 C \n"
"ATOM 19 O VAL A 7 5.413 -49.867 0.054 1.00 8.60 O \n"
"ATOM 20 CB VAL A 7 6.465 -49.587 2.995 1.00 12.36 C \n"
"ATOM 21 CG1 VAL A 7 7.822 -49.808 2.438 1.00 13.83 C \n"
"ATOM 22 CG2 VAL A 7 6.065 -48.116 2.797 1.00 9.85 C \n"
"ATOM 23 N ALA A 8 3.529 -49.593 1.197 1.00 13.39 N \n"
"ATOM 24 CA ALA A 8 2.773 -49.057 0.069 1.00 13.79 C \n"
"ATOM 25 C ALA A 8 2.602 -47.552 0.172 1.00 9.25 C \n"
"ATOM 26 O ALA A 8 2.500 -47.028 1.279 1.00 15.37 O \n"
"ATOM 27 CB ALA A 8 1.448 -49.689 0.031 1.00 12.95 C \n"
"ATOM 28 N THR A 9 2.586 -46.876 -0.980 1.00 11.17 N \n"
"ATOM 29 CA THR A 9 2.309 -45.447 -1.099 1.00 9.76 C \n"
"ATOM 30 C THR A 9 1.358 -45.161 -2.252 1.00 11.27 C \n"
"ATOM 31 O THR A 9 1.157 -46.000 -3.122 1.00 11.74 O \n"
"ATOM 32 CB THR A 9 3.557 -44.649 -1.423 1.00 16.25 C \n"
"ATOM 33 OG1 THR A 9 4.402 -45.395 -2.311 1.00 16.45 O \n"
"ATOM 34 CG2 THR A 9 4.289 -44.276 -0.187 1.00 21.89 C \n"
"ATOM 35 N ASP A 10 0.912 -43.916 -2.338 1.00 10.94 N \n"
"ATOM 36 CA ASP A 10 0.087 -43.441 -3.442 1.00 13.74 C \n"
"ATOM 37 C ASP A 10 0.911 -43.463 -4.735 1.00 15.06 C \n"
"ATOM 38 O ASP A 10 2.125 -43.629 -4.690 1.00 19.02 O \n"
"ATOM 39 CB ASP A 10 -0.369 -41.999 -3.147 1.00 15.41 C \n"
"ATOM 40 CG ASP A 10 -1.770 -41.707 -3.633 1.00 19.42 C \n"
"ATOM 41 OD1 ASP A 10 -2.203 -42.274 -4.658 1.00 21.59 O \n"
"ATOM 42 OD2 ASP A 10 -2.450 -40.884 -2.985 1.00 25.31 O \n"
"ATOM 43 N THR A 11 0.258 -43.262 -5.878 1.00 15.47 N \n"
"ATOM 44 CA THR A 11 0.955 -43.164 -7.162 1.00 17.91 C \n"
"ATOM 45 C THR A 11 1.383 -41.737 -7.432 1.00 13.11 C \n"
"ATOM 46 O THR A 11 2.346 -41.509 -8.165 1.00 17.17 O \n"
"ATOM 47 CB THR A 11 0.069 -43.624 -8.337 1.00 19.89 C \n"
"ATOM 48 OG1 THR A 11 -1.219 -43.985 -7.840 1.00 26.13 O \n"
"ATOM 49 CG2 THR A 11 0.670 -44.827 -9.035 1.00 24.20 C \n"
"ATOM 50 N ALA A 12 0.597 -40.783 -6.944 1.00 10.88 N \n"
"ATOM 51 CA ALA A 12 1.015 -39.392 -6.880 1.00 15.07 C \n"
"ATOM 52 C ALA A 12 0.247 -38.601 -5.834 1.00 16.92 C \n"
"ATOM 53 O ALA A 12 -0.957 -38.376 -5.971 1.00 18.82 O \n"
"ATOM 54 CB ALA A 12 0.851 -38.739 -8.220 1.00 17.27 C \n"
"ATOM 55 N PHE A 13 0.976 -38.090 -4.852 1.00 12.98 N \n"
"ATOM 56 CA PHE A 13 0.439 -37.164 -3.870 1.00 16.31 C \n"
"ATOM 57 C PHE A 13 1.552 -36.139 -3.617 1.00 15.19 C \n"
"ATOM 58 O PHE A 13 2.357 -36.311 -2.714 1.00 16.10 O \n"
"ATOM 59 CB PHE A 13 0.072 -37.936 -2.585 1.00 15.61 C \n"
"ATOM 60 CG PHE A 13 -0.553 -37.084 -1.485 1.00 21.35 C \n"
"ATOM 61 CD1 PHE A 13 -1.391 -36.012 -1.784 1.00 22.62 C \n"
"ATOM 62 CD2 PHE A 13 -0.343 -37.401 -0.138 1.00 22.88 C \n"
"ATOM 63 CE1 PHE A 13 -2.008 -35.280 -0.759 1.00 23.34 C \n"
"ATOM 64 CE2 PHE A 13 -0.954 -36.674 0.890 1.00 19.43 C \n"
"ATOM 65 CZ PHE A 13 -1.786 -35.616 0.582 1.00 21.44 C \n"
"ATOM 66 N VAL A 14 1.688 -35.161 -4.509 1.00 10.89 N \n"
"ATOM 67 CA VAL A 14 2.776 -34.186 -4.429 1.00 9.30 C \n"
"ATOM 68 C VAL A 14 2.595 -33.225 -3.228 1.00 9.34 C \n"
"ATOM 69 O VAL A 14 1.506 -32.751 -2.953 1.00 9.03 O \n"
"ATOM 70 CB VAL A 14 2.855 -33.367 -5.740 1.00 11.74 C \n"
"ATOM 71 CG1 VAL A 14 3.946 -32.344 -5.654 1.00 12.55 C \n"
"ATOM 72 CG2 VAL A 14 3.097 -34.263 -6.929 1.00 14.44 C \n"
"ATOM 73 N PRO A 15 3.665 -32.948 -2.479 1.00 12.35 N \n"
"ATOM 74 CA PRO A 15 5.036 -33.449 -2.569 1.00 11.72 C \n"
"ATOM 75 C PRO A 15 5.379 -34.583 -1.577 1.00 13.93 C \n"
"ATOM 76 O PRO A 15 6.533 -34.744 -1.195 1.00 18.82 O \n"
"ATOM 77 CB PRO A 15 5.845 -32.202 -2.289 1.00 5.84 C \n"
"ATOM 78 CG PRO A 15 5.035 -31.517 -1.262 1.00 9.84 C \n"
"ATOM 79 CD PRO A 15 3.580 -31.870 -1.485 1.00 10.51 C \n"
"ATOM 80 N PHE A 16 4.402 -35.387 -1.186 1.00 8.41 N \n"
"ATOM 81 CA PHE A 16 4.666 -36.483 -0.284 1.00 8.06 C \n"
"ATOM 82 C PHE A 16 5.243 -37.743 -0.959 1.00 9.43 C \n"
"ATOM 83 O PHE A 16 6.202 -38.330 -0.453 1.00 8.42 O \n"
"ATOM 84 CB PHE A 16 3.396 -36.818 0.461 1.00 13.56 C \n"
"ATOM 85 CG PHE A 16 2.973 -35.765 1.423 1.00 12.62 C \n"
"ATOM 86 CD1 PHE A 16 2.157 -34.730 1.015 1.00 19.89 C \n"
"ATOM 87 CD2 PHE A 16 3.354 -35.829 2.747 1.00 13.73 C \n"
"ATOM 88 CE1 PHE A 16 1.727 -33.767 1.923 1.00 16.04 C \n"
"ATOM 89 CE2 PHE A 16 2.927 -34.885 3.645 1.00 13.91 C \n"
"ATOM 90 CZ PHE A 16 2.114 -33.853 3.232 1.00 14.41 C \n"
"ATOM 91 N GLU A 17 4.682 -38.144 -2.097 1.00 12.52 N \n"
"ATOM 92 CA GLU A 17 5.309 -39.136 -2.968 1.00 6.67 C \n"
"ATOM 93 C GLU A 17 4.919 -38.967 -4.435 1.00 5.89 C \n"
"ATOM 94 O GLU A 17 3.741 -38.853 -4.764 1.00 8.72 O \n"
"ATOM 95 CB GLU A 17 4.959 -40.549 -2.512 1.00 8.35 C \n"
"ATOM 96 CG GLU A 17 3.459 -40.852 -2.452 1.00 8.92 C \n"
"ATOM 97 CD GLU A 17 2.821 -40.477 -1.131 1.00 12.62 C \n"
"ATOM 98 OE1 GLU A 17 3.519 -40.401 -0.107 1.00 9.84 O \n"
"ATOM 99 OE2 GLU A 17 1.599 -40.280 -1.108 1.00 12.75 O \n"
"ATOM 100 N PHE A 18 5.911 -38.937 -5.320 1.00 5.14 N \n"
"ATOM 101 CA PHE A 18 5.660 -38.911 -6.757 1.00 9.50 C \n"
"ATOM 102 C PHE A 18 6.898 -39.324 -7.527 1.00 10.39 C \n"
"ATOM 103 O PHE A 18 8.011 -39.141 -7.067 1.00 17.79 O \n"
"ATOM 104 CB PHE A 18 5.218 -37.514 -7.199 1.00 11.65 C \n"
"ATOM 105 CG PHE A 18 6.210 -36.421 -6.860 1.00 16.07 C \n"
"ATOM 106 CD1 PHE A 18 6.411 -36.029 -5.547 1.00 10.03 C \n"
"ATOM 107 CD2 PHE A 18 6.983 -35.835 -7.852 1.00 13.69 C \n"
"ATOM 108 CE1 PHE A 18 7.358 -35.084 -5.225 1.00 10.95 C \n"
"ATOM 109 CE2 PHE A 18 7.924 -34.894 -7.533 1.00 11.46 C \n"
"ATOM 110 CZ PHE A 18 8.111 -34.519 -6.218 1.00 13.40 C \n"
"ATOM 111 N LYS A 19 6.688 -39.933 -8.679 1.00 17.27 N \n"
"ATOM 112 CA LYS A 19 7.757 -40.517 -9.483 1.00 18.53 C \n"
"ATOM 113 C LYS A 19 8.684 -39.410 -9.874 1.00 16.86 C \n"
"ATOM 114 O LYS A 19 8.246 -38.277 -10.033 1.00 23.82 O \n"
"ATOM 115 CB LYS A 19 7.172 -41.134 -10.760 1.00 19.89 C \n"
"ATOM 116 CG LYS A 19 7.690 -42.510 -11.172 1.00 22.98 C \n"
"ATOM 117 CD LYS A 19 6.811 -43.079 -12.310 1.00 32.56 C \n"
"ATOM 118 CE LYS A 19 7.493 -43.024 -13.707 1.00 37.16 C \n"
"ATOM 119 NZ LYS A 19 8.111 -44.366 -14.175 1.00 43.17 N \n"
"ATOM 120 N GLN A 20 9.933 -39.765 -10.149 1.00 17.99 N \n"
"ATOM 121 CA GLN A 20 10.913 -38.819 -10.646 1.00 18.84 C \n"
"ATOM 122 C GLN A 20 11.956 -39.566 -11.453 1.00 22.14 C \n"
"ATOM 123 O GLN A 20 12.839 -40.223 -10.906 1.00 19.00 O \n"
"ATOM 124 CB GLN A 20 11.576 -38.108 -9.489 1.00 25.85 C \n"
"ATOM 125 CG GLN A 20 12.681 -37.175 -9.906 1.00 34.40 C \n"
"ATOM 126 CD GLN A 20 12.430 -35.762 -9.438 1.00 40.67 C \n"
"ATOM 127 OE1 GLN A 20 11.338 -35.204 -9.642 1.00 36.36 O \n"
"ATOM 128 NE2 GLN A 20 13.444 -35.159 -8.806 1.00 43.33 N \n"
"ATOM 129 N GLY A 21 11.838 -39.490 -12.770 1.00 25.64 N \n"
"ATOM 130 CA GLY A 21 12.625 -40.363 -13.613 1.00 24.65 C \n"
"ATOM 131 C GLY A 21 12.170 -41.774 -13.349 1.00 22.51 C \n"
"ATOM 132 O GLY A 21 10.966 -42.067 -13.451 1.00 26.14 O \n"
"ATOM 133 N ASP A 22 13.064 -42.542 -12.728 1.00 24.83 N \n"
"ATOM 134 CA ASP A 22 12.844 -43.972 -12.478 1.00 28.01 C \n"
"ATOM 135 C ASP A 22 12.513 -44.316 -11.018 1.00 26.08 C \n"
"ATOM 136 O ASP A 22 12.033 -45.405 -10.736 1.00 28.92 O \n"
"ATOM 137 CB ASP A 22 14.080 -44.759 -12.922 1.00 29.85 C \n"
"ATOM 138 CG ASP A 22 13.760 -45.856 -13.932 1.00 31.93 C \n"
"ATOM 139 OD1 ASP A 22 12.647 -45.842 -14.519 1.00 29.44 O \n"
"ATOM 140 OD2 ASP A 22 14.649 -46.714 -14.153 1.00 30.85 O \n"
"ATOM 141 N LEU A 23 12.812 -43.409 -10.097 1.00 21.05 N \n"
"ATOM 142 CA LEU A 23 12.541 -43.628 -8.680 1.00 21.62 C \n"
"ATOM 143 C LEU A 23 11.271 -42.910 -8.193 1.00 21.36 C \n"
"ATOM 144 O LEU A 23 10.470 -42.421 -8.992 1.00 18.41 O \n"
"ATOM 145 CB LEU A 23 13.758 -43.207 -7.821 1.00 23.15 C \n"
"ATOM 146 CG LEU A 23 14.539 -41.903 -8.077 1.00 27.51 C \n"
"ATOM 147 CD1 LEU A 23 13.584 -40.747 -7.901 1.00 35.59 C \n"
"ATOM 148 CD2 LEU A 23 15.749 -41.723 -7.120 1.00 24.86 C \n"
"ATOM 149 N TYR A 24 11.059 -42.944 -6.881 1.00 19.66 N \n"
"ATOM 150 CA TYR A 24 10.053 -42.139 -6.222 1.00 11.94 C \n"
"ATOM 151 C TYR A 24 10.743 -41.202 -5.271 1.00 12.46 C \n"
"ATOM 152 O TYR A 24 11.758 -41.550 -4.684 1.00 12.11 O \n"
"ATOM 153 CB TYR A 24 9.105 -43.013 -5.440 1.00 8.67 C \n"
"ATOM 154 CG TYR A 24 7.833 -43.272 -6.173 1.00 13.15 C \n"
"ATOM 155 CD1 TYR A 24 7.824 -44.054 -7.328 1.00 12.14 C \n"
"ATOM 156 CD2 TYR A 24 6.634 -42.705 -5.745 1.00 16.31 C \n"
"ATOM 157 CE1 TYR A 24 6.659 -44.262 -8.039 1.00 14.20 C \n"
"ATOM 158 CE2 TYR A 24 5.455 -42.899 -6.461 1.00 15.50 C \n"
"ATOM 159 CZ TYR A 24 5.481 -43.675 -7.608 1.00 16.96 C \n"
"ATOM 160 OH TYR A 24 4.339 -43.828 -8.353 1.00 21.52 O \n"
"ATOM 161 N VAL A 25 10.100 -40.076 -5.007 1.00 12.67 N \n"
"ATOM 162 CA VAL A 25 10.667 -39.003 -4.203 1.00 14.06 C \n"
"ATOM 163 C VAL A 25 9.494 -38.373 -3.409 1.00 15.53 C \n"
"ATOM 164 O VAL A 25 8.338 -38.545 -3.795 1.00 11.06 O \n"
"ATOM 165 CB VAL A 25 11.318 -37.926 -5.136 1.00 16.19 C \n"
"ATOM 166 CG1 VAL A 25 11.840 -36.788 -4.347 1.00 21.62 C \n"
"ATOM 167 CG2 VAL A 25 12.444 -38.515 -5.922 1.00 16.97 C \n"
"ATOM 168 N GLY A 26 9.800 -37.659 -2.316 1.00 11.81 N \n"
"ATOM 169 CA GLY A 26 8.794 -36.947 -1.548 1.00 14.13 C \n"
"ATOM 170 C GLY A 26 9.090 -36.916 -0.055 1.00 12.53 C \n"
"ATOM 171 O GLY A 26 10.047 -37.507 0.401 1.00 13.15 O \n"
"ATOM 172 N PHE A 27 8.255 -36.250 0.722 1.00 6.71 N \n"
"ATOM 173 CA PHE A 27 8.449 -36.150 2.157 1.00 6.44 C \n"
"ATOM 174 C PHE A 27 8.265 -37.513 2.867 1.00 13.51 C \n"
"ATOM 175 O PHE A 27 8.938 -37.810 3.855 1.00 11.16 O \n"
"ATOM 176 CB PHE A 27 7.466 -35.105 2.678 1.00 6.47 C \n"
"ATOM 177 CG PHE A 27 7.433 -34.976 4.155 1.00 9.33 C \n"
"ATOM 178 CD1 PHE A 27 6.661 -35.833 4.922 1.00 9.03 C \n"
"ATOM 179 CD2 PHE A 27 8.193 -34.013 4.788 1.00 11.46 C \n"
"ATOM 180 CE1 PHE A 27 6.652 -35.747 6.305 1.00 8.35 C \n"
"ATOM 181 CE2 PHE A 27 8.193 -33.913 6.166 1.00 8.19 C \n"
"ATOM 182 CZ PHE A 27 7.421 -34.789 6.929 1.00 10.12 C \n"
"ATOM 183 N ASP A 28 7.220 -38.241 2.470 1.00 14.07 N \n"
"ATOM 184 CA ASP A 28 6.920 -39.574 2.993 1.00 14.99 C \n"
"ATOM 185 C ASP A 28 8.018 -40.545 2.622 1.00 14.48 C \n"
"ATOM 186 O ASP A 28 8.456 -41.330 3.450 1.00 16.21 O \n"
"ATOM 187 CB ASP A 28 5.619 -40.098 2.402 1.00 13.40 C \n"
"ATOM 188 CG ASP A 28 4.416 -39.662 3.173 1.00 12.04 C \n"
"ATOM 189 OD1 ASP A 28 4.554 -39.091 4.260 1.00 12.89 O \n"
"ATOM 190 OD2 ASP A 28 3.309 -39.880 2.689 1.00 8.53 O \n"
"ATOM 191 N VAL A 29 8.486 -40.451 1.382 1.00 4.87 N \n"
"ATOM 192 CA VAL A 29 9.555 -41.299 0.886 1.00 11.18 C \n"
"ATOM 193 C VAL A 29 10.903 -41.070 1.570 1.00 11.07 C \n"
"ATOM 194 O VAL A 29 11.591 -42.030 1.891 1.00 17.10 O \n"
"ATOM 195 CB VAL A 29 9.694 -41.172 -0.632 1.00 9.96 C \n"
"ATOM 196 CG1 VAL A 29 10.821 -42.039 -1.122 1.00 14.26 C \n"
"ATOM 197 CG2 VAL A 29 8.416 -41.617 -1.303 1.00 8.50 C \n"
"ATOM 198 N ASP A 30 11.244 -39.824 1.881 1.00 15.02 N \n"
"ATOM 199 CA ASP A 30 12.423 -39.537 2.702 1.00 10.85 C \n"
"ATOM 200 C ASP A 30 12.219 -39.839 4.180 1.00 14.35 C \n"
"ATOM 201 O ASP A 30 13.172 -40.144 4.880 1.00 16.20 O \n"
"ATOM 202 CB ASP A 30 12.834 -38.080 2.571 1.00 14.69 C \n"
"ATOM 203 CG ASP A 30 13.384 -37.757 1.226 1.00 16.86 C \n"
"ATOM 204 OD1 ASP A 30 13.872 -38.658 0.537 1.00 19.60 O \n"
"ATOM 205 OD2 ASP A 30 13.371 -36.579 0.858 1.00 20.02 O \n"
"ATOM 206 N LEU A 31 10.996 -39.679 4.673 1.00 10.19 N \n"
"ATOM 207 CA LEU A 31 10.713 -39.909 6.075 1.00 9.62 C \n"
"ATOM 208 C LEU A 31 10.804 -41.366 6.448 1.00 7.52 C \n"
"ATOM 209 O LEU A 31 11.319 -41.694 7.497 1.00 14.41 O \n"
"ATOM 210 CB LEU A 31 9.331 -39.398 6.443 1.00 12.00 C \n"
"ATOM 211 CG LEU A 31 9.047 -39.590 7.930 1.00 12.23 C \n"
"ATOM 212 CD1 LEU A 31 9.826 -38.576 8.725 1.00 18.71 C \n"
"ATOM 213 CD2 LEU A 31 7.593 -39.413 8.203 1.00 15.30 C \n"
"ATOM 214 N TRP A 32 10.214 -42.233 5.646 1.00 6.24 N \n"
"ATOM 215 CA TRP A 32 10.280 -43.646 5.923 1.00 6.70 C \n"
"ATOM 216 C TRP A 32 11.717 -44.182 5.856 1.00 10.70 C \n"
"ATOM 217 O TRP A 32 12.102 -45.034 6.653 1.00 15.23 O \n"
"ATOM 218 CB TRP A 32 9.395 -44.418 4.950 1.00 8.19 C \n"
"ATOM 219 CG TRP A 32 9.486 -45.874 5.160 1.00 6.64 C \n"
"ATOM 220 CD1 TRP A 32 10.044 -46.779 4.313 1.00 9.05 C \n"
"ATOM 221 CD2 TRP A 32 9.212 -46.576 6.375 1.00 7.01 C \n"
"ATOM 222 NE1 TRP A 32 10.168 -47.998 4.931 1.00 7.95 N \n"
"ATOM 223 CE2 TRP A 32 9.663 -47.906 6.200 1.00 9.49 C \n"
"ATOM 224 CE3 TRP A 32 8.640 -46.210 7.607 1.00 11.61 C \n"
"ATOM 225 CZ2 TRP A 32 9.568 -48.874 7.210 1.00 8.00 C \n"
"ATOM 226 CZ3 TRP A 32 8.545 -47.174 8.618 1.00 6.35 C \n"
"ATOM 227 CH2 TRP A 32 9.011 -48.488 8.411 1.00 8.04 C \n"
"";
const char* gbpFrag2String = ""
"ATOM 80 N PHE A 16 4.402 -35.387 -1.186 1.00 8.41 N \n"
"ATOM 81 CA PHE A 16 4.666 -36.483 -0.284 1.00 8.06 C \n"
"ATOM 82 C PHE A 16 5.243 -37.743 -0.959 1.00 9.43 C \n"
"ATOM 83 O PHE A 16 6.202 -38.330 -0.453 1.00 8.42 O \n"
"ATOM 84 CB PHE A 16 3.396 -36.818 0.461 1.00 13.56 C \n"
"ATOM 85 CG PHE A 16 2.973 -35.765 1.423 1.00 12.62 C \n"
"ATOM 86 CD1 PHE A 16 2.157 -34.730 1.015 1.00 19.89 C \n"
"ATOM 87 CD2 PHE A 16 3.354 -35.829 2.747 1.00 13.73 C \n"
"ATOM 88 CE1 PHE A 16 1.727 -33.767 1.923 1.00 16.04 C \n"
"ATOM 89 CE2 PHE A 16 2.927 -34.885 3.645 1.00 13.91 C \n"
"ATOM 90 CZ PHE A 16 2.114 -33.853 3.232 1.00 14.41 C \n"
"ATOM 91 N GLU A 17 4.682 -38.144 -2.097 1.00 12.52 N \n"
"ATOM 92 CA GLU A 17 5.309 -39.136 -2.968 1.00 6.67 C \n"
"ATOM 93 C GLU A 17 4.919 -38.967 -4.435 1.00 5.89 C \n"
"ATOM 94 O GLU A 17 3.741 -38.853 -4.764 1.00 8.72 O \n"
"ATOM 95 CB GLU A 17 4.959 -40.549 -2.512 1.00 8.35 C \n"
"ATOM 96 CG GLU A 17 3.459 -40.852 -2.452 1.00 8.92 C \n"
"ATOM 97 CD GLU A 17 2.821 -40.477 -1.131 1.00 12.62 C \n"
"ATOM 98 OE1 GLU A 17 3.519 -40.401 -0.107 1.00 9.84 O \n"
"ATOM 99 OE2 GLU A 17 1.599 -40.280 -1.108 1.00 12.75 O \n"
"ATOM 100 N PHE A 18 5.911 -38.937 -5.320 1.00 5.14 N \n"
"ATOM 101 CA PHE A 18 5.660 -38.911 -6.757 1.00 9.50 C \n"
"ATOM 102 C PHE A 18 6.898 -39.324 -7.527 1.00 10.39 C \n"
"ATOM 103 O PHE A 18 8.011 -39.141 -7.067 1.00 17.79 O \n"
"ATOM 104 CB PHE A 18 5.218 -37.514 -7.199 1.00 11.65 C \n"
"ATOM 105 CG PHE A 18 6.210 -36.421 -6.860 1.00 16.07 C \n"
"ATOM 106 CD1 PHE A 18 6.411 -36.029 -5.547 1.00 10.03 C \n"
"ATOM 107 CD2 PHE A 18 6.983 -35.835 -7.852 1.00 13.69 C \n"
"ATOM 108 CE1 PHE A 18 7.358 -35.084 -5.225 1.00 10.95 C \n"
"ATOM 109 CE2 PHE A 18 7.924 -34.894 -7.533 1.00 11.46 C \n"
"ATOM 110 CZ PHE A 18 8.111 -34.519 -6.218 1.00 13.40 C \n"
"ATOM 111 N LYS A 19 6.688 -39.933 -8.679 1.00 17.27 N \n"
"ATOM 112 CA LYS A 19 7.757 -40.517 -9.483 1.00 18.53 C \n"
"ATOM 113 C LYS A 19 8.684 -39.410 -9.874 1.00 16.86 C \n"
"ATOM 114 O LYS A 19 8.246 -38.277 -10.033 1.00 23.82 O \n"
"ATOM 115 CB LYS A 19 7.172 -41.134 -10.760 1.00 19.89 C \n"
"ATOM 116 CG LYS A 19 7.690 -42.510 -11.172 1.00 22.98 C \n"
"ATOM 117 CD LYS A 19 6.811 -43.079 -12.310 1.00 32.56 C \n"
"ATOM 118 CE LYS A 19 7.493 -43.024 -13.707 1.00 37.16 C \n"
"ATOM 119 NZ LYS A 19 8.111 -44.366 -14.175 1.00 43.17 N \n"
"";
std::string pdbString(gbpFrag1String);
std::istringstream inFileStream( pdbString );
PdbStructure pdbStructure(inFileStream, PdbStructure::InputType::PDB);
// Protein myProtein("LVVATDTAFVPFEFKQGDLYVGFDVDLW");
Protein myProtein(pdbStructure);
Compound::AtomTargetLocations atomTargets = myProtein.createAtomTargets(pdbStructure);
cout << "Number of atom targets found = " << atomTargets.size() << endl;
cout << "Number of atoms = " << myProtein.getNumAtoms() << endl;
// just for testing
// myProtein.matchDefaultConfiguration(atomTargets, Compound::Match_Idealized);
Real residual = myProtein.getTransformAndResidual(atomTargets).residual;
cout << "residual = " << residual << endl;
// Write pdb files for visual comparison
cout << pdbString << endl;
// Use a different chain id for matched structure
myProtein.setPdbChainId("B");
myProtein.writeDefaultPdb(cout, myProtein.getTopLevelTransform());
// Increased target residual from 0.05 to 0.06 after raising tolerance in ObservedPointFitter call
// Raises actual residual to 0.052
//SimTK_ASSERT_ALWAYS(residual < 0.08, (String("RMS error was too large: ") + String(residual)).c_str());
// SCF raised this further, on 7 april 2021:
SimTK_ASSERT_ALWAYS(residual < 0.15, (String("RMS error was too large: ") + String(residual)).c_str());
}
int main()
{
SimTK_START_TEST("TestProteinDihedrals");
SimTK_SUBTEST(testProteinDihedrals);
SimTK_END_TEST();
}
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