Extracting Atoms using make_ndx or select

User discussions
1

GROMACS version:2022.2
GROMACS modification: No

Hi @jalemkul @hess

I have been trying to use gmx make_ndx and gmx select to extract from a base pdb for making an index file.
Seems both the option doesn’t give the correct atoms associated to the residue. Is this a known phenomenon of Gromacs or am I the only one who is facing this problem?
I don’t see any reason to have problem associated with the pdb itself as I could perform a successful docking and md simulation (Gromacs) using same pdb.

Here are the pdb coordinates which has 463 Atoms but the gmx make_ndx shows only 238 Atoms
ATOM 1 N PRO R 1 -3.139 -3.631 5.525 1.00 53.54 N
ATOM 2 CA PRO R 1 -3.365 -4.690 4.537 1.00 30.21 C
ATOM 3 C PRO R 1 -2.069 -5.163 3.887 1.00 10.51 C
ATOM 4 O PRO R 1 -1.095 -4.414 3.805 1.00 5.55 O
ATOM 5 CB PRO R 1 -4.271 -4.022 3.500 1.00 43.50 C
ATOM 6 CG PRO R 1 -3.975 -2.566 3.621 1.00 63.55 C
ATOM 7 CD PRO R 1 -3.654 -2.328 5.070 1.00 11.21 C
ATOM 15 N LEU R 2 -2.506 -6.305 3.113 1.00 60.15 N
ATOM 16 CA LEU R 2 -1.329 -6.878 2.468 1.00 1.45 C
ATOM 17 C LEU R 2 -1.138 -6.299 1.070 1.00 3.01 C
ATOM 18 O LEU R 2 -2.074 -5.802 0.444 1.00 70.11 O
ATOM 19 CB LEU R 2 -1.456 -8.400 2.390 1.00 41.01 C
ATOM 20 CG LEU R 2 -1.973 -8.963 1.066 1.00 52.14 C
ATOM 21 CD1 LEU R 2 -0.827 -9.527 0.241 1.00 25.43 C
ATOM 22 CD2 LEU R 2 -3.029 -10.030 1.316 1.00 64.13 C
ATOM 34 N PRO R 3 0.218 -6.335 0.609 1.00 13.35 N
ATOM 35 CA PRO R 3 0.560 -5.825 -0.721 1.00 44.15 C
ATOM 36 C PRO R 3 -0.044 -6.669 -1.839 1.00 2.42 C
ATOM 37 O PRO R 3 -0.023 -7.898 -1.781 1.00 71.24 O
ATOM 38 CB PRO R 3 2.088 -5.912 -0.752 1.00 63.01 C
ATOM 39 CG PRO R 3 2.426 -6.989 0.220 1.00 11.24 C
ATOM 40 CD PRO R 3 1.382 -6.914 1.300 1.00 2.43 C
ATOM 48 N ASP R 4 -0.447 -5.797 -2.998 1.00 5.31 N
ATOM 49 CA ASP R 4 -1.055 -6.486 -4.130 1.00 14.32 C
ATOM 50 C ASP R 4 0.011 -6.978 -5.104 1.00 14.13 C
ATOM 51 O ASP R 4 -0.027 -8.123 -5.555 1.00 43.11 O
ATOM 52 CB ASP R 4 -2.035 -5.559 -4.852 1.00 5.32 C
ATOM 53 CG ASP R 4 -2.555 -4.454 -3.954 1.00 34.14 C
ATOM 54 OD1 ASP R 4 -3.515 -4.708 -3.195 1.00 70.34 O
ATOM 55 OD2 ASP R 4 -2.003 -3.336 -4.008 1.00 10.40 O
ATOM 60 N CYS R 5 1.101 -6.351 -5.172 1.00 32.03 N
ATOM 61 CA CYS R 5 2.177 -6.695 -6.093 1.00 72.12 C
ATOM 62 C CYS R 5 2.948 -7.916 -5.598 1.00 54.51 C
ATOM 63 O CYS R 5 3.480 -8.692 -6.392 1.00 53.32 O
ATOM 64 CB CYS R 5 3.130 -5.510 -6.262 1.00 60.32 C
ATOM 65 SG CYS R 5 2.293 -3.915 -6.530 1.00 12.35 S
ATOM 70 N CYS R 6 2.765 -8.160 -4.173 1.00 10.24 N
ATOM 71 CA CYS R 6 3.470 -9.285 -3.570 1.00 11.31 C
ATOM 72 C CYS R 6 2.727 -10.593 -3.826 1.00 52.41 C
ATOM 73 O CYS R 6 3.332 -11.663 -3.874 1.00 64.42 O
ATOM 74 CB CYS R 6 3.633 -9.064 -2.065 1.00 33.23 C
ATOM 75 SG CYS R 6 5.332 -9.312 -1.456 1.00 72.23 S
ATOM 80 N ARG R 7 0.955 -10.172 -4.354 1.00 24.10 N
ATOM 81 CA ARG R 7 0.129 -11.347 -4.604 1.00 43.03 C
ATOM 82 C ARG R 7 0.211 -11.767 -6.069 1.00 25.31 C
ATOM 83 O ARG R 7 0.271 -12.956 -6.380 1.00 73.51 O
ATOM 84 CB ARG R 7 -1.325 -11.064 -4.225 1.00 34.24 C
ATOM 85 CG ARG R 7 -2.313 -12.058 -4.815 1.00 0.44 C
ATOM 86 CD ARG R 7 -3.283 -11.379 -5.769 1.00 41.11 C
ATOM 87 NE ARG R 7 -4.585 -11.143 -5.150 1.00 45.43 N
ATOM 88 CZ ARG R 7 -5.563 -10.460 -5.735 1.00 30.23 C
ATOM 89 NH1 ARG R 7 -5.388 -9.950 -6.946 1.00 13.11 N
ATOM 90 NH2 ARG R 7 -6.720 -10.288 -5.107 1.00 45.54 N
ATOM 104 N GLN R 8 1.637 -11.576 -6.423 1.00 71.33 N
ATOM 105 CA GLN R 8 1.710 -11.845 -7.855 1.00 4.04 C
ATOM 106 C GLN R 8 3.138 -11.683 -8.366 1.00 61.41 C
ATOM 107 O GLN R 8 3.425 -11.951 -9.533 1.00 61.31 O
ATOM 108 CB GLN R 8 0.773 -10.909 -8.619 1.00 50.04 C
ATOM 109 CG GLN R 8 -0.640 -10.872 -8.059 1.00 43.12 C
ATOM 110 CD GLN R 8 -1.699 -10.931 -9.142 1.00 63.13 C
ATOM 111 OE1 GLN R 8 -2.622 -11.744 -9.080 1.00 42.33 O
ATOM 112 NE2 GLN R 8 -1.571 -10.068 -10.143 1.00 52.12 N
ATOM 121 N LYS R 9 3.712 -10.847 -7.423 1.00 24.03 N
ATOM 122 CA LYS R 9 5.111 -10.650 -7.784 1.00 3.04 C
ATOM 123 C LYS R 9 5.233 -9.799 -9.044 1.00 24.31 C
ATOM 124 O LYS R 9 6.024 -10.104 -9.938 1.00 21.15 O
ATOM 125 CB LYS R 9 5.799 -12.000 -7.998 1.00 61.13 C
ATOM 126 CG LYS R 9 6.238 -12.671 -6.708 1.00 42.12 C
ATOM 127 CD LYS R 9 7.711 -13.041 -6.746 1.00 23.52 C
ATOM 128 CE LYS R 9 8.207 -13.493 -5.381 1.00 5.24 C
ATOM 129 NZ LYS R 9 9.538 -12.909 -5.053 1.00 73.02 N
ATOM 143 N THR R 10 4.257 -8.720 -9.323 1.00 55.31 N
ATOM 144 CA THR R 10 4.277 -7.825 -10.473 1.00 51.13 C
ATOM 145 C THR R 10 4.943 -6.498 -10.126 1.00 61.53 C
ATOM 146 O THR R 10 5.239 -5.691 -11.008 1.00 34.02 O
ATOM 147 CB THR R 10 2.854 -7.551 -10.997 1.00 4.51 C
ATOM 148 OG1 THR R 10 2.260 -6.475 -10.261 1.00 24.52 O
ATOM 149 CG2 THR R 10 1.985 -8.793 -10.879 1.00 63.52 C
ATOM 157 N CYS R 11 4.869 -6.090 -8.891 1.00 31.10 N
ATOM 158 CA CYS R 11 5.501 -4.861 -8.427 1.00 31.25 C
ATOM 159 C CYS R 11 5.980 -5.007 -6.985 1.00 70.10 C
ATOM 160 O CYS R 11 5.707 -6.012 -6.328 1.00 3.40 O
ATOM 161 CB CYS R 11 4.524 -3.688 -8.535 1.00 24.42 C
ATOM 162 SG CYS R 11 4.115 -2.912 -6.938 1.00 75.44 S
ATOM 167 N SER R 12 6.815 -4.192 -6.381 1.00 23.20 N
ATOM 168 CA SER R 12 7.336 -4.209 -5.019 1.00 14.11 C
ATOM 169 C SER R 12 6.198 -4.265 -4.004 1.00 23.05 C
ATOM 170 O SER R 12 5.115 -3.727 -4.236 1.00 63.33 O
ATOM 171 CB SER R 12 8.200 -2.972 -4.765 1.00 61.45 C
ATOM 172 OG SER R 12 9.365 -2.991 -5.572 1.00 41.51 O
ATOM 178 N CYS R 13 6.339 -4.965 -2.886 1.00 24.23 N
ATOM 179 CA CYS R 13 5.339 -5.094 -1.833 1.00 53.43 C
ATOM 180 C CYS R 13 5.388 -3.897 -0.887 1.00 75.24 C
ATOM 181 O CYS R 13 4.362 -3.468 -0.359 1.00 34.30 O
ATOM 182 CB CYS R 13 5.558 -6.388 -1.048 1.00 34.13 C
ATOM 183 SG CYS R 13 6.480 -7.666 -1.962 1.00 11.30 S
ATOM 188 N ARG R 14 6.674 -3.514 -0.518 1.00 74.21 N
ATOM 189 CA ARG R 14 6.857 -2.368 0.364 1.00 32.34 C
ATOM 190 C ARG R 14 6.251 -1.109 -0.247 1.00 51.44 C
ATOM 191 O ARG R 14 6.290 -0.033 0.352 1.00 21.43 O
ATOM 192 CB ARG R 14 8.344 -2.147 0.646 1.00 41.12 C
ATOM 193 CG ARG R 14 8.610 -1.251 1.845 1.00 65.43 C
ATOM 194 CD ARG R 14 9.726 -1.805 2.717 1.00 62.41 C
ATOM 195 NE ARG R 14 11.015 -1.190 2.413 1.00 3.11 N
ATOM 196 CZ ARG R 14 12.157 -1.555 2.986 1.00 50.13 C
ATOM 197 NH1 ARG R 14 12.169 -2.527 3.887 1.00 64.31 N
ATOM 198 NH2 ARG R 14 13.290 -0.947 2.657 1.00 54.03 N
ATOM 212 N LEU R 15 5.954 -1.140 -1.475 1.00 53.42 N
ATOM 213 CA LEU R 15 5.339 -0.013 -2.169 1.00 65.13 C
ATOM 214 C LEU R 15 4.265 0.639 -1.305 1.00 73.41 C
ATOM 215 O LEU R 15 4.102 1.859 -1.314 1.00 72.04 O
ATOM 216 CB LEU R 15 4.733 -0.475 -3.495 1.00 50.05 C
ATOM 217 CG LEU R 15 3.227 -0.742 -3.488 1.00 64.20 C
ATOM 218 CD1 LEU R 15 2.692 -0.822 -4.909 1.00 65.14 C
ATOM 219 CD2 LEU R 15 2.917 -2.022 -2.726 1.00 72.55 C
ATOM 231 N TYR R 16 3.447 -0.102 -0.634 1.00 14.41 N
ATOM 232 CA TYR R 16 2.387 0.395 0.236 1.00 21.44 C
ATOM 233 C TYR R 16 2.961 1.259 1.355 1.00 21.52 C
ATOM 234 O TYR R 16 2.369 2.266 1.741 1.00 22.24 O
ATOM 235 CB TYR R 16 1.599 -0.773 0.832 1.00 73.02 C
ATOM 236 CG TYR R 16 2.408 -1.629 1.780 1.00 73.12 C
ATOM 237 CD1 TYR R 16 2.759 -1.162 3.040 1.00 24.14 C
ATOM 238 CD2 TYR R 16 2.821 -2.904 1.415 1.00 63.31 C
ATOM 239 CE1 TYR R 16 3.499 -1.940 3.910 1.00 61.33 C
ATOM 240 CE2 TYR R 16 3.560 -3.690 2.278 1.00 31.03 C
ATOM 241 CZ TYR R 16 3.897 -3.204 3.524 1.00 15.43 C
ATOM 242 OH TYR R 16 4.633 -3.983 4.387 1.00 44.33 O
ATOM 252 N GLU R 17 4.055 0.758 1.950 1.00 65.25 N
ATOM 253 CA GLU R 17 4.710 1.495 3.024 1.00 30.32 C
ATOM 254 C GLU R 17 5.011 2.928 2.596 1.00 11.23 C
ATOM 255 O GLU R 17 4.974 3.852 3.410 1.00 20.03 O
ATOM 256 CB GLU R 17 6.004 0.792 3.439 1.00 5.44 C
ATOM 257 CG GLU R 17 6.092 0.509 4.929 1.00 21.45 C
ATOM 258 CD GLU R 17 6.666 1.673 5.712 1.00 4.34 C
ATOM 259 OE1 GLU R 17 7.344 2.524 5.100 1.00 51.45 O
ATOM 260 OE2 GLU R 17 6.438 1.733 6.939 1.00 53.22 O
ATOM 267 N LEU R 18 5.541 3.068 1.421 1.00 0.21 N
ATOM 268 CA LEU R 18 5.849 4.389 0.883 1.00 22.24 C
ATOM 269 C LEU R 18 4.696 5.358 1.125 1.00 70.45 C
ATOM 270 O LEU R 18 4.884 6.434 1.693 1.00 32.02 O
ATOM 271 CB LEU R 18 6.147 4.295 -0.614 1.00 74.32 C
ATOM 272 CG LEU R 18 7.533 3.771 -0.992 1.00 34.33 C
ATOM 273 CD1 LEU R 18 7.544 2.250 -1.000 1.00 22.02 C
ATOM 274 CD2 LEU R 18 7.958 4.316 -2.347 1.00 2.41 C
ATOM 286 N LEU R 19 3.508 5.127 0.492 1.00 64.03 N
ATOM 287 CA LEU R 19 2.323 5.960 0.662 1.00 30.13 C
ATOM 288 C LEU R 19 1.766 5.831 2.076 1.00 33.23 C
ATOM 289 O LEU R 19 1.110 6.742 2.582 1.00 2.32 O
ATOM 290 CB LEU R 19 1.251 5.571 -0.358 1.00 4.41 C
ATOM 291 CG LEU R 19 0.138 4.656 0.153 1.00 1.44 C
ATOM 292 CD1 LEU R 19 -1.108 5.464 0.482 1.00 2.01 C
ATOM 293 CD2 LEU R 19 -0.178 3.577 -0.872 1.00 15.51 C
ATOM 305 N HIS R 20 1.973 4.722 2.787 1.00 3.34 N
ATOM 306 CA HIS R 20 1.501 4.475 4.145 1.00 72.10 C
ATOM 307 C HIS R 20 2.321 5.267 5.159 1.00 62.04 C
ATOM 308 O HIS R 20 1.930 5.405 6.317 1.00 54.44 O
ATOM 309 CB HIS R 20 1.572 2.982 4.468 1.00 2.34 C
ATOM 310 CG HIS R 20 0.367 2.214 4.020 1.00 22.01 C
ATOM 311 ND1 HIS R 20 -0.486 1.574 4.895 1.00 45.14 N
ATOM 312 CD2 HIS R 20 -0.127 1.986 2.781 1.00 41.33 C
ATOM 313 CE1 HIS R 20 -1.451 0.984 4.212 1.00 10.55 C
ATOM 314 NE2 HIS R 20 -1.257 1.220 2.927 1.00 22.33 N
ATOM 322 N GLY R 21 3.395 5.834 4.515 1.00 34.52 N
ATOM 323 CA GLY R 21 4.252 6.604 5.396 1.00 3.24 C
ATOM 324 C GLY R 21 4.285 8.075 5.032 1.00 3.35 C
ATOM 325 O GLY R 21 4.259 8.939 5.909 1.00 63.03 O
ATOM 329 N ALA R 22 4.347 8.378 3.365 1.00 55.40 N
ATOM 330 CA ALA R 22 4.383 9.755 2.887 1.00 10.04 C
ATOM 331 C ALA R 22 2.998 10.223 2.454 1.00 33.40 C
ATOM 332 O ALA R 22 2.840 11.322 1.924 1.00 25.31 O
ATOM 333 CB ALA R 22 5.371 9.889 1.738 1.00 71.11 C
ATOM 339 N GLY R 23 1.992 9.294 2.847 1.00 21.35 N
ATOM 340 CA GLY R 23 0.633 9.639 2.474 1.00 60.35 C
ATOM 341 C GLY R 23 -0.395 8.738 3.128 1.00 30.42 C
ATOM 342 O GLY R 23 -1.321 8.262 2.472 1.00 10.54 O
ATOM 346 N ASN R 24 -0.153 8.684 4.585 1.00 51.43 N
ATOM 347 CA ASN R 24 -1.074 7.832 5.328 1.00 24.21 C
ATOM 348 C ASN R 24 -2.455 8.472 5.419 1.00 13.40 C
ATOM 349 O ASN R 24 -3.476 7.791 5.315 1.00 64.21 O
ATOM 350 CB ASN R 24 -0.531 7.563 6.733 1.00 64.40 C
ATOM 351 CG ASN R 24 0.128 8.785 7.342 1.00 1.23 C
ATOM 352 OD1 ASN R 24 -0.549 9.702 7.807 1.00 52.33 O
ATOM 353 ND2 ASN R 24 1.456 8.803 7.343 1.00 51.22 N
ATOM 360 N HIS R 25 -2.574 9.901 5.225 1.00 14.23 N
ATOM 361 CA HIS R 25 -3.831 10.635 5.329 1.00 61.20 C
ATOM 362 C HIS R 25 -4.623 10.542 4.028 1.00 1.33 C
ATOM 363 O HIS R 25 -5.852 10.601 4.033 1.00 31.24 O
ATOM 364 CB HIS R 25 -3.563 12.100 5.674 1.00 53.24 C
ATOM 365 CG HIS R 25 -4.527 12.667 6.670 1.00 33.20 C
ATOM 366 ND1 HIS R 25 -4.737 14.020 6.828 1.00 14.42 N
ATOM 367 CD2 HIS R 25 -5.341 12.055 7.561 1.00 35.52 C
ATOM 368 CE1 HIS R 25 -5.638 14.216 7.775 1.00 43.31 C
ATOM 369 NE2 HIS R 25 -6.021 13.039 8.236 1.00 43.24 N
ATOM 377 N ALA R 26 -3.951 9.990 3.067 1.00 50.31 N
ATOM 378 CA ALA R 26 -4.587 9.889 1.760 1.00 74.54 C
ATOM 379 C ALA R 26 -5.578 8.730 1.720 1.00 14.20 C
ATOM 380 O ALA R 26 -6.625 8.818 1.079 1.00 51.11 O
ATOM 381 CB ALA R 26 -3.536 9.723 0.672 1.00 10.42 C
ATOM 387 N ALA R 27 -5.104 7.812 2.796 1.00 41.00 N
ATOM 388 CA ALA R 27 -5.965 6.637 2.840 1.00 30.23 C
ATOM 389 C ALA R 27 -7.006 6.761 3.948 1.00 71.54 C
ATOM 390 O ALA R 27 -8.119 6.251 3.826 1.00 32.33 O
ATOM 391 CB ALA R 27 -5.132 5.379 3.035 1.00 24.20 C
ATOM 397 N GLY R 28 -6.601 7.631 4.999 1.00 11.04 N
ATOM 398 CA GLY R 28 -7.515 7.808 6.113 1.00 4.41 C
ATOM 399 C GLY R 28 -8.714 8.660 5.749 1.00 53.21 C
ATOM 400 O GLY R 28 -9.828 8.404 6.208 1.00 41.11 O
ATOM 404 N ILE R 29 -8.744 9.129 4.315 1.00 3.55 N
ATOM 405 CA ILE R 29 -9.815 10.022 3.891 1.00 32.21 C
ATOM 406 C ILE R 29 -10.493 9.504 2.627 1.00 13.31 C
ATOM 407 O ILE R 29 -11.713 9.599 2.480 1.00 23.23 O
ATOM 408 CB ILE R 29 -9.292 11.447 3.633 1.00 42.04 C
ATOM 409 CG1 ILE R 29 -8.964 12.141 4.956 1.00 14.41 C
ATOM 410 CG2 ILE R 29 -10.314 12.252 2.845 1.00 54.04 C
ATOM 411 CD1 ILE R 29 -8.411 11.206 6.008 1.00 3.33 C
ATOM 423 N LEU R 30 -9.583 8.148 2.075 1.00 31.31 N
ATOM 424 CA LEU R 30 -10.106 7.612 0.823 1.00 51.32 C
ATOM 425 C LEU R 30 -11.199 6.581 1.086 1.00 51.44 C
ATOM 426 O LEU R 30 -12.193 6.515 0.361 1.00 65.52 O
ATOM 427 CB LEU R 30 -8.978 6.980 0.005 1.00 34.34 C
ATOM 428 CG LEU R 30 -8.173 7.934 -0.877 1.00 63.53 C
ATOM 429 CD1 LEU R 30 -6.894 7.265 -1.357 1.00 5.14 C
ATOM 430 CD2 LEU R 30 -9.009 8.400 -2.060 1.00 64.23 C
ATOM 442 N THR R 31 -10.896 6.367 2.511 1.00 3.51 N
ATOM 443 CA THR R 31 -11.865 5.341 2.871 1.00 74.31 C
ATOM 444 C THR R 31 -12.847 5.854 3.917 1.00 15.45 C
ATOM 445 O THR R 31 -14.029 5.508 3.898 1.00 73.30 O
ATOM 446 CB THR R 31 -11.171 4.077 3.412 1.00 62.22 C
ATOM 447 OG1 THR R 31 -12.150 3.100 3.782 1.00 31.10 O
ATOM 448 CG2 THR R 31 -10.300 4.410 4.614 1.00 52.21 C
ATOM 456 N LEU R 32 -12.122 6.049 5.057 1.00 33.12 N
ATOM 457 CA LEU R 32 -12.957 6.612 6.113 1.00 72.13 C
ATOM 458 C LEU R 32 -13.233 5.577 7.199 1.00 2.31 C
ATOM 459 O LEU R 32 -12.735 5.685 8.318 1.00 2.05 O
ATOM 460 CB LEU R 32 -14.277 7.120 5.530 1.00 60.02 C
ATOM 461 CG LEU R 32 -14.694 8.532 5.943 1.00 62.01 C
ATOM 462 CD1 LEU R 32 -13.842 9.570 5.230 1.00 43.24 C
ATOM 463 CD2 LEU R 32 -16.170 8.759 5.651 1.00 1.11 C

output of gmx make_ndx
gmx make_ndx -f test.pdb -o 1.ndx

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 32 Protein residues
Analysing Protein…

0 System : 238 atoms
1 Protein : 238 atoms
2 Protein-H : 238 atoms
3 C-alpha : 32 atoms
4 Backbone : 96 atoms
5 MainChain : 128 atoms
6 MainChain+Cb : 157 atoms
7 MainChain+H : 128 atoms
8 SideChain : 110 atoms
9 SideChain-H : 110 atoms

How to fix this?
`

2

There appears to be missing atoms in your pdb listing - for instance between atom 7 and atom 15.

A command like grep '^ATOM ' protein.pdb | wc -l could help counting the actual number of ATOM lines

3

Indeed. The pdb seems to be the system with the hydrogen atoms removed.

4

@hess @ebriand Thanks.
@jalemkul Just curious to know the a few things,

  1. If few atoms are missing, still can I run MD simulation?

  2. gmx make_ndx will not extract correct atoms from the provided pdb if some atoms are missing.
    eg: in above provided pdb Res 7 (ARG) contains atoms from 80 to 90. So If I use make_ndx for res 7 will I get the same atoms (80-90)?

  3. What is the process to extract atoms based on the hierarchy mode (Chain, Res, Atom) in multichain system?
    for eg I want to extract atoms of (Res 8 of Chain A) and atoms of (Res 10 of Chain B).

Thanks