diff --git a/examples/1crn.gro b/examples/1crn.gro new file mode 100644 index 0000000000000000000000000000000000000000..84896264cfbe94278664d6c91156b63eeaf7001a --- /dev/null +++ b/examples/1crn.gro @@ -0,0 +1,330 @@ +CRAMBIN + 327 + 1THR N 1 1.705 1.410 0.363 + 1THR CA 2 1.697 1.278 0.434 + 1THR C 3 1.569 1.276 0.513 + 1THR O 4 1.527 1.383 0.559 + 1THR CB 5 1.817 1.270 0.534 + 1THR OG1 6 1.933 1.283 0.446 + 1THR CG2 7 1.815 1.155 0.630 + 2THR N 8 1.512 1.156 0.526 + 2THR CA 9 1.386 1.147 0.607 + 2THR C 10 1.416 1.079 0.738 + 2THR O 11 1.499 0.986 0.744 + 2THR CB 12 1.273 1.071 0.526 + 2THR OG1 13 1.331 0.944 0.493 + 2THR CG2 14 1.248 1.144 0.389 + 3CYS N 15 1.349 1.124 0.842 + 3CYS CA 16 1.366 1.071 0.979 + 3CYS C 17 1.227 1.043 1.032 + 3CYS O 18 1.139 1.131 1.018 + 3CYS CB 19 1.437 1.175 1.069 + 3CYS SG 20 1.589 1.243 1.002 + 4CYS N 21 1.202 0.927 1.093 + 4CYS CA 22 1.065 0.899 1.141 + 4CYS C 23 1.065 0.879 1.292 + 4CYS O 24 1.166 0.830 1.349 + 4CYS CB 25 1.006 0.775 1.068 + 4CYS SG 26 0.984 0.802 0.890 + 5PRO N 27 0.956 0.911 1.356 + 5PRO CA 28 0.945 0.903 1.501 + 5PRO C 29 0.929 0.767 1.561 + 5PRO O 30 0.949 0.752 1.682 + 5PRO CB 31 0.823 0.996 1.535 + 5PRO CG 32 0.734 0.979 1.411 + 5PRO CD 33 0.837 0.980 1.296 + 6SER N 34 0.887 0.669 1.480 + 6SER CA 35 0.867 0.531 1.528 + 6SER C 36 0.875 0.438 1.408 + 6SER O 37 0.873 0.486 1.292 + 6SER CB 38 0.734 0.512 1.600 + 6SER OG 39 0.627 0.522 1.503 + 7ILE N 40 0.888 0.308 1.436 + 7ILE CA 41 0.891 0.208 1.326 + 7ILE C 42 0.758 0.209 1.251 + 7ILE O 43 0.767 0.203 1.125 + 7ILE CB 44 0.921 0.068 1.392 + 7ILE CG1 45 1.071 0.070 1.431 + 7ILE CG2 46 0.881 -0.048 1.297 + 7ILE CD1 47 1.118 -0.052 1.514 + 8VAL N 48 0.646 0.216 1.316 + 8VAL CA 49 0.515 0.221 1.245 + 8VAL C 50 0.512 0.338 1.146 + 8VAL O 51 0.466 0.327 1.034 + 8VAL CB 52 0.400 0.235 1.348 + 8VAL CG1 53 0.272 0.289 1.287 + 8VAL CG2 54 0.376 0.103 1.421 + 9ALA N 55 0.561 0.455 1.194 + 9ALA CA 56 0.560 0.577 1.108 + 9ALA C 57 0.644 0.553 0.985 + 9ALA O 58 0.605 0.593 0.874 + 9ALA CB 59 0.602 0.698 1.189 + 10ARG N 60 0.765 0.491 1.000 + 10ARG CA 61 0.850 0.461 0.884 + 10ARG C 62 0.780 0.361 0.788 + 10ARG O 63 0.788 0.378 0.665 + 10ARG CB 64 0.985 0.402 0.930 + 10ARG CG 65 1.075 0.361 0.815 + 10ARG CD 66 1.123 0.470 0.724 + 10ARG NE 67 1.214 0.557 0.803 + 10ARG CZ 68 1.276 0.661 0.744 + 10ARG NH1 69 1.254 0.693 0.616 + 10ARG NH2 70 1.360 0.732 0.820 + 11SER N 71 0.719 0.258 0.845 + 11SER CA 72 0.650 0.158 0.757 + 11SER C 73 0.538 0.231 0.677 + 11SER O 74 0.521 0.202 0.556 + 11SER CB 75 0.591 0.046 0.840 + 11SER OG 76 0.699 -0.027 0.901 + 12ASN N 77 0.465 0.318 0.745 + 12ASN CA 78 0.354 0.394 0.675 + 12ASN C 79 0.411 0.485 0.569 + 12ASN O 80 0.354 0.500 0.462 + 12ASN CB 81 0.266 0.468 0.775 + 12ASN CG 82 0.180 0.373 0.861 + 12ASN OD1 83 0.157 0.261 0.817 + 12ASN ND2 84 0.139 0.425 0.977 + 13PHE N 85 0.526 0.550 0.600 + 13PHE CA 86 0.593 0.636 0.506 + 13PHE C 87 0.630 0.558 0.380 + 13PHE O 88 0.614 0.607 0.265 + 13PHE CB 89 0.718 0.699 0.575 + 13PHE CG 90 0.788 0.801 0.488 + 13PHE CD1 91 0.891 0.759 0.403 + 13PHE CD2 92 0.753 0.937 0.498 + 13PHE CE1 93 0.956 0.854 0.319 + 13PHE CE2 94 0.818 1.028 0.414 + 13PHE CZ 95 0.914 0.984 0.329 + 14ASN N 96 0.690 0.439 0.399 + 14ASN CA 97 0.733 0.361 0.279 + 14ASN C 98 0.612 0.321 0.191 + 14ASN O 99 0.624 0.314 0.068 + 14ASN CB 100 0.814 0.240 0.324 + 14ASN CG 101 0.956 0.286 0.373 + 14ASN OD1 102 1.001 0.389 0.332 + 14ASN ND2 103 1.012 0.196 0.454 + 15VAL N 104 0.499 0.293 0.257 + 15VAL CA 105 0.378 0.260 0.174 + 15VAL C 106 0.330 0.387 0.100 + 15VAL O 107 0.295 0.382 -0.019 + 15VAL CB 108 0.270 0.195 0.261 + 15VAL CG1 109 0.138 0.183 0.181 + 15VAL CG2 110 0.317 0.053 0.301 + 16CYS N 111 0.332 0.499 0.172 + 16CYS CA 112 0.289 0.628 0.113 + 16CYS C 113 0.369 0.660 -0.011 + 16CYS O 114 0.320 0.715 -0.110 + 16CYS CB 115 0.304 0.737 0.224 + 16CYS SG 116 0.256 0.901 0.165 + 17ARG N 117 0.500 0.623 -0.010 + 17ARG CA 118 0.590 0.649 -0.121 + 17ARG C 119 0.574 0.556 -0.241 + 17ARG O 120 0.623 0.590 -0.351 + 17ARG CB 121 0.737 0.651 -0.073 + 17ARG CG 122 0.772 0.769 0.021 + 17ARG CD 123 0.795 0.895 -0.062 + 17ARG NE 124 0.921 0.886 -0.134 + 17ARG CZ 125 0.954 0.953 -0.243 + 17ARG NH1 126 0.866 1.035 -0.303 + 17ARG NH2 127 1.079 0.949 -0.290 + 18LEU N 128 0.505 0.441 -0.220 + 18LEU CA 129 0.493 0.343 -0.333 + 18LEU C 130 0.440 0.401 -0.462 + 18LEU O 131 0.499 0.375 -0.569 + 18LEU CB 132 0.420 0.218 -0.286 + 18LEU CG 133 0.496 0.118 -0.199 + 18LEU CD1 134 0.391 0.010 -0.163 + 18LEU CD2 135 0.613 0.061 -0.277 + 19PRO N 136 0.333 0.479 -0.454 + 19PRO CA 137 0.279 0.538 -0.580 + 19PRO C 138 0.357 0.654 -0.632 + 19PRO O 139 0.326 0.705 -0.742 + 19PRO CB 140 0.136 0.577 -0.547 + 19PRO CG 141 0.122 0.569 -0.399 + 19PRO CD 142 0.242 0.494 -0.341 + 20GLY N 143 0.456 0.705 -0.556 + 20GLY CA 144 0.537 0.819 -0.602 + 20GLY C 145 0.501 0.948 -0.528 + 20GLY O 146 0.553 1.051 -0.573 + 21THR N 147 0.418 0.944 -0.426 + 21THR CA 148 0.377 1.061 -0.351 + 21THR C 149 0.502 1.140 -0.304 + 21THR O 150 0.595 1.076 -0.252 + 21THR CB 151 0.299 1.019 -0.222 + 21THR OG1 152 0.205 0.914 -0.262 + 21THR CG2 153 0.226 1.135 -0.155 + 22PRO N 154 0.497 1.270 -0.318 + 22PRO CA 155 0.614 1.351 -0.270 + 22PRO C 156 0.640 1.323 -0.123 + 22PRO O 157 0.549 1.306 -0.038 + 22PRO CB 158 0.570 1.497 -0.292 + 22PRO CG 159 0.468 1.489 -0.400 + 22PRO CD 160 0.396 1.357 -0.381 + 23GLU N 161 0.773 1.330 -0.092 + 23GLU CA 162 0.811 1.310 0.050 + 23GLU C 163 0.743 1.407 0.141 + 23GLU O 164 0.704 1.368 0.254 + 23GLU CB 165 0.965 1.329 0.066 + 23GLU CG 166 1.044 1.209 0.006 + 23GLU CD 167 1.194 1.217 0.039 + 23GLU OE1 168 1.242 1.322 0.068 + 23GLU OE2 169 1.254 1.107 0.029 + 24ALA N 170 0.721 1.533 0.097 + 24ALA CA 171 0.661 1.632 0.191 + 24ALA C 172 0.521 1.594 0.235 + 24ALA O 173 0.478 1.617 0.350 + 24ALA CB 174 0.660 1.770 0.125 + 25ILE N 175 0.444 1.532 0.140 + 25ILE CA 176 0.307 1.489 0.176 + 25ILE C 177 0.308 1.364 0.264 + 25ILE O 178 0.231 1.352 0.358 + 25ILE CB 179 0.220 1.464 0.046 + 25ILE CG1 180 0.182 1.605 -0.013 + 25ILE CG2 181 0.090 1.386 0.081 + 25ILE CD1 182 0.076 1.676 0.076 + 26CYS N 183 0.403 1.276 0.231 + 26CYS CA 184 0.418 1.155 0.319 + 26CYS C 185 0.463 1.194 0.460 + 26CYS O 186 0.423 1.125 0.555 + 26CYS CB 187 0.504 1.052 0.254 + 26CYS SG 188 0.435 0.979 0.102 + 27ALA N 189 0.541 1.301 0.469 + 27ALA CA 190 0.588 1.350 0.603 + 27ALA C 191 0.470 1.391 0.688 + 27ALA O 192 0.453 1.342 0.803 + 27ALA CB 193 0.688 1.462 0.583 + 28THR N 194 0.383 1.480 0.636 + 28THR CA 195 0.269 1.522 0.719 + 28THR C 196 0.167 1.413 0.743 + 28THR O 197 0.095 1.411 0.847 + 28THR CB 198 0.199 1.652 0.661 + 28THR OG1 199 0.166 1.622 0.523 + 28THR CG2 200 0.291 1.774 0.670 + 29TYR N 201 0.162 1.319 0.651 + 29TYR CA 202 0.072 1.204 0.666 + 29TYR C 203 0.112 1.112 0.781 + 29TYR O 204 0.029 1.063 0.854 + 29TYR CB 205 0.075 1.123 0.532 + 29TYR CG 206 -0.020 1.004 0.535 + 29TYR CD1 207 -0.155 1.034 0.564 + 29TYR CD2 208 0.019 0.875 0.510 + 29TYR CE1 209 -0.250 0.933 0.567 + 29TYR CE2 210 -0.080 0.771 0.516 + 29TYR CZ 211 -0.208 0.803 0.543 + 29TYR OH 212 -0.310 0.706 0.546 + 30THR N 213 0.247 1.098 0.799 + 30THR CA 214 0.299 0.999 0.895 + 30THR C 215 0.361 1.051 1.023 + 30THR O 216 0.377 0.971 1.119 + 30THR CB 217 0.408 0.910 0.822 + 30THR OG1 218 0.512 1.003 0.782 + 30THR CG2 219 0.349 0.832 0.703 + 31GLY N 220 0.398 1.176 1.024 + 31GLY CA 221 0.477 1.234 1.136 + 31GLY C 222 0.626 1.224 1.111 + 31GLY O 223 0.704 1.275 1.195 + 32CYS N 224 0.671 1.163 0.999 + 32CYS CA 225 0.814 1.169 0.964 + 32CYS C 226 0.850 1.314 0.921 + 32CYS O 227 0.758 1.395 0.894 + 32CYS CB 228 0.850 1.069 0.853 + 32CYS SG 229 0.805 0.899 0.888 + 33ILE N 230 0.979 1.341 0.917 + 33ILE CA 231 1.028 1.476 0.882 + 33ILE C 232 1.135 1.466 0.774 + 33ILE O 233 1.197 1.358 0.755 + 33ILE CB 234 1.079 1.554 1.008 + 33ILE CG1 235 1.206 1.480 1.067 + 33ILE CG2 236 0.968 1.569 1.114 + 33ILE CD1 237 1.273 1.568 1.178 + 34ILE N 238 1.149 1.577 0.704 + 34ILE CA 239 1.255 1.588 0.604 + 34ILE C 240 1.359 1.692 0.656 + 34ILE O 241 1.317 1.801 0.695 + 34ILE CB 242 1.199 1.636 0.468 + 34ILE CG1 243 1.091 1.534 0.416 + 34ILE CG2 244 1.313 1.652 0.363 + 34ILE CD1 245 1.015 1.602 0.294 + 35ILE N 246 1.486 1.649 0.654 + 35ILE CA 247 1.593 1.745 0.694 + 35ILE C 248 1.691 1.755 0.582 + 35ILE O 249 1.710 1.666 0.497 + 35ILE CB 250 1.662 1.699 0.828 + 35ILE CG1 251 1.736 1.565 0.807 + 35ILE CG2 252 1.559 1.697 0.943 + 35ILE CD1 253 1.830 1.521 0.922 + 36PRO N 254 1.766 1.867 0.581 + 36PRO CA 255 1.863 1.886 0.474 + 36PRO C 256 1.992 1.804 0.495 + 36PRO O 257 2.059 1.774 0.394 + 36PRO CB 258 1.895 2.036 0.478 + 36PRO CG 259 1.824 2.094 0.591 + 36PRO CD 260 1.737 1.990 0.660 + 37GLY N 261 2.017 1.773 0.622 + 37GLY CA 262 2.145 1.697 0.651 + 37GLY C 263 2.114 1.548 0.643 + 37GLY O 264 2.014 1.502 0.588 + 38ALA N 265 2.205 1.470 0.703 + 38ALA CA 266 2.202 1.324 0.702 + 38ALA C 267 2.194 1.263 0.840 + 38ALA O 268 2.187 1.139 0.844 + 38ALA CB 269 2.325 1.270 0.627 + 39THR N 270 2.189 1.344 0.944 + 39THR CA 271 2.194 1.291 1.081 + 39THR C 272 2.062 1.319 1.152 + 39THR O 273 2.036 1.432 1.195 + 39THR CB 274 2.313 1.360 1.159 + 39THR OG1 275 2.428 1.340 1.071 + 39THR CG2 276 2.334 1.293 1.296 + 40CYS N 277 1.983 1.211 1.164 + 40CYS CA 278 1.850 1.231 1.230 + 40CYS C 279 1.868 1.245 1.378 + 40CYS O 280 1.953 1.172 1.436 + 40CYS CB 281 1.758 1.112 1.200 + 40CYS SG 282 1.720 1.093 1.024 + 41PRO N 283 1.788 1.327 1.443 + 41PRO CA 284 1.792 1.342 1.588 + 41PRO C 285 1.739 1.221 1.659 + 41PRO O 286 1.665 1.137 1.603 + 41PRO CB 287 1.708 1.466 1.615 + 41PRO CG 288 1.610 1.469 1.500 + 41PRO CD 289 1.686 1.415 1.378 + 42GLY N 290 1.773 1.212 1.788 + 42GLY CA 291 1.733 1.096 1.869 + 42GLY C 292 1.587 1.069 1.887 + 42GLY O 293 1.543 0.955 1.917 + 43ASP N 294 1.504 1.175 1.872 + 43ASP CA 295 1.356 1.157 1.884 + 43ASP C 296 1.294 1.123 1.747 + 43ASP O 297 1.172 1.104 1.743 + 43ASP CB 298 1.293 1.274 1.958 + 43ASP CG 299 1.314 1.409 1.896 + 43ASP OD1 300 1.411 1.430 1.821 + 43ASP OD2 301 1.227 1.496 1.926 + 44TYR N 302 1.372 1.117 1.643 + 44TYR CA 303 1.326 1.074 1.508 + 44TYR C 304 1.428 0.969 1.461 + 44TYR O 305 1.493 0.986 1.357 + 44TYR CB 306 1.320 1.191 1.407 + 44TYR CG 307 1.200 1.282 1.440 + 44TYR CD1 308 1.212 1.385 1.533 + 44TYR CD2 309 1.077 1.262 1.376 + 44TYR CE1 310 1.105 1.467 1.561 + 44TYR CE2 311 0.968 1.343 1.405 + 44TYR CZ 312 0.980 1.446 1.500 + 44TYR OH 313 0.874 1.526 1.527 + 45ALA N 314 1.434 0.864 1.542 + 45ALA CA 315 1.544 0.767 1.525 + 45ALA C 316 1.517 0.653 1.428 + 45ALA O 317 1.609 0.571 1.404 + 45ALA CB 318 1.568 0.710 1.668 + 46ASN N 319 1.397 0.650 1.374 + 46ASN CA 320 1.351 0.539 1.288 + 46ASN C 321 1.331 0.585 1.145 + 46ASN O 322 1.373 0.693 1.103 + 46ASN CB 323 1.227 0.477 1.350 + 46ASN CG 324 1.254 0.430 1.492 + 46ASN OD1 325 1.198 0.485 1.589 + 46ASN ND2 326 1.341 0.330 1.502 + 46ASN OXT 327 1.270 0.497 1.075 + 4.09600 1.86500 2.25180 0.00000 0.00000 0.00000 0.00000 -0.03026 0.00000 \ No newline at end of file diff --git a/examples/test.gro b/examples/test.gro new file mode 100644 index 0000000000000000000000000000000000000000..64233f4818620923ab08828ef26b0ceb02213fbf --- /dev/null +++ b/examples/test.gro @@ -0,0 +1,9 @@ +MD of 2 waters, t= 4.2 + 6 + 1WATER OW1 1 0.126 1.624 1.679 0.1227 -0.0580 0.0434 + 1WATER HW2 2 0.190 1.661 1.747 0.8085 0.3191 -0.7791 + 1WATER HW3 3 0.177 1.568 1.613 -0.9045 -2.6469 1.3180 + 2WATER OW1 4 1.275 0.053 0.622 0.2519 0.3140 -0.1734 + 2WATER HW2 5 1.337 0.002 0.680 -1.0641 -1.1349 0.0257 + 2WATER HW3 6 1.326 0.120 0.568 1.9427 -0.8216 -0.0244 + 1.82060 1.82060 1.82060 \ No newline at end of file