From 65433359078eaeb48dd7fb7cc833f596d6992703 Mon Sep 17 00:00:00 2001 From: Maohua Yang Date: Wed, 16 Oct 2024 17:56:57 +0800 Subject: [PATCH] Support for protein-protein complex (#57) * feat: support protein-protein complex calculation * version 0.1.7 --- .gitignore | 5 + ChangeLog.txt | 4 + example/protein-protein/1vf6_LIG.pdb | 494 +++++++++++++++++++++++++++ example/protein-protein/1vf6_REC.pdb | 477 ++++++++++++++++++++++++++ example/protein-protein/default.ini | 59 ++++ example/protein-protein/run.sh | 10 + tests/test_pipline.py | 8 +- unigbsa/pipeline.py | 29 +- unigbsa/simulation/mdrun.py | 7 +- unigbsa/simulation/topology.py | 24 +- unigbsa/simulation/utils.py | 23 ++ unigbsa/utils.py | 64 +++- unigbsa/version.py | 2 +- 13 files changed, 1177 insertions(+), 29 deletions(-) create mode 100644 ChangeLog.txt create mode 100644 example/protein-protein/1vf6_LIG.pdb create mode 100644 example/protein-protein/1vf6_REC.pdb create mode 100644 example/protein-protein/default.ini create mode 100644 example/protein-protein/run.sh diff --git a/.gitignore b/.gitignore index ff33b03..ee2070c 100644 --- a/.gitignore +++ b/.gitignore @@ -127,3 +127,8 @@ dmypy.json # Pyre type checker .pyre/ + + +# examples +example/3f/#* +example/3f/complex_reres.pdb diff --git a/ChangeLog.txt b/ChangeLog.txt new file mode 100644 index 0000000..78d9c75 --- /dev/null +++ b/ChangeLog.txt @@ -0,0 +1,4 @@ +Changes in Release 0.1.7 +-------------------------------------------------------------------------------- +* Uni-GBSA now support calculation for protein-protein complexes +* Fix some code styles. \ No newline at end of file diff --git a/example/protein-protein/1vf6_LIG.pdb b/example/protein-protein/1vf6_LIG.pdb new file mode 100644 index 0000000..75330fb --- /dev/null +++ b/example/protein-protein/1vf6_LIG.pdb @@ -0,0 +1,494 @@ +ATOM 478 N LEU B 10 34.803 -11.532 -16.288 1.00 73.88 N +ATOM 479 CA LEU B 10 35.023 -12.538 -17.365 1.00 72.43 C +ATOM 480 C LEU B 10 36.433 -13.135 -17.278 1.00 70.58 C +ATOM 481 O LEU B 10 36.669 -14.242 -17.752 1.00 69.56 O +ATOM 482 CB LEU B 10 34.815 -11.890 -18.741 1.00 73.20 C +ATOM 483 CG LEU B 10 34.878 -12.826 -19.950 1.00 73.69 C +ATOM 484 CD1 LEU B 10 33.664 -13.738 -19.936 1.00 74.72 C +ATOM 485 CD2 LEU B 10 34.916 -12.024 -21.240 1.00 73.79 C +ATOM 486 N GLN B 11 37.362 -12.402 -16.668 1.00 68.06 N +ATOM 487 CA GLN B 11 38.738 -12.875 -16.526 1.00 65.18 C +ATOM 488 C GLN B 11 38.817 -14.206 -15.779 1.00 61.67 C +ATOM 489 O GLN B 11 39.480 -15.139 -16.232 1.00 59.70 O +ATOM 490 CB GLN B 11 39.595 -11.825 -15.813 1.00 68.06 C +ATOM 491 CG GLN B 11 39.929 -10.622 -16.681 1.00 73.21 C +ATOM 492 CD GLN B 11 38.703 -9.808 -17.087 1.00 77.44 C +ATOM 493 OE1 GLN B 11 38.699 -9.160 -18.140 1.00 80.01 O +ATOM 494 NE2 GLN B 11 37.664 -9.823 -16.247 1.00 77.72 N +ATOM 495 N VAL B 12 38.144 -14.296 -14.636 1.00 56.35 N +ATOM 496 CA VAL B 12 38.153 -15.537 -13.876 1.00 53.43 C +ATOM 497 C VAL B 12 37.694 -16.695 -14.770 1.00 51.39 C +ATOM 498 O VAL B 12 38.212 -17.804 -14.656 1.00 49.02 O +ATOM 499 CB VAL B 12 37.239 -15.454 -12.625 1.00 53.52 C +ATOM 500 CG1 VAL B 12 37.073 -16.829 -12.008 1.00 52.37 C +ATOM 501 CG2 VAL B 12 37.854 -14.509 -11.598 1.00 55.40 C +ATOM 502 N LEU B 13 36.735 -16.436 -15.661 1.00 47.63 N +ATOM 503 CA LEU B 13 36.248 -17.477 -16.561 1.00 45.49 C +ATOM 504 C LEU B 13 37.285 -17.793 -17.631 1.00 44.24 C +ATOM 505 O LEU B 13 37.435 -18.948 -18.029 1.00 42.59 O +ATOM 506 CB LEU B 13 34.939 -17.061 -17.238 1.00 45.65 C +ATOM 507 CG LEU B 13 33.687 -16.911 -16.371 1.00 47.07 C +ATOM 508 CD1 LEU B 13 32.511 -16.596 -17.274 1.00 48.10 C +ATOM 509 CD2 LEU B 13 33.414 -18.188 -15.603 1.00 48.45 C +ATOM 510 N GLN B 14 37.993 -16.767 -18.097 1.00 43.63 N +ATOM 511 CA GLN B 14 39.022 -16.963 -19.114 1.00 46.79 C +ATOM 512 C GLN B 14 40.177 -17.743 -18.513 1.00 43.91 C +ATOM 513 O GLN B 14 40.698 -18.663 -19.128 1.00 45.48 O +ATOM 514 CB GLN B 14 39.543 -15.624 -19.643 1.00 49.92 C +ATOM 515 CG GLN B 14 38.497 -14.787 -20.359 1.00 56.71 C +ATOM 516 CD GLN B 14 39.096 -13.557 -21.013 1.00 61.55 C +ATOM 517 OE1 GLN B 14 39.812 -12.781 -20.368 1.00 63.50 O +ATOM 518 NE2 GLN B 14 38.804 -13.367 -22.298 1.00 61.54 N +ATOM 519 N VAL B 15 40.568 -17.356 -17.309 1.00 42.78 N +ATOM 520 CA VAL B 15 41.650 -18.008 -16.596 1.00 42.57 C +ATOM 521 C VAL B 15 41.311 -19.479 -16.406 1.00 42.79 C +ATOM 522 O VAL B 15 42.144 -20.359 -16.633 1.00 39.52 O +ATOM 523 CB VAL B 15 41.873 -17.351 -15.212 1.00 43.39 C +ATOM 524 CG1 VAL B 15 42.837 -18.177 -14.385 1.00 44.29 C +ATOM 525 CG2 VAL B 15 42.414 -15.934 -15.392 1.00 45.40 C +ATOM 526 N LEU B 16 40.073 -19.742 -16.004 1.00 41.02 N +ATOM 527 CA LEU B 16 39.634 -21.107 -15.780 1.00 42.33 C +ATOM 528 C LEU B 16 39.626 -21.902 -17.092 1.00 42.18 C +ATOM 529 O LEU B 16 39.988 -23.080 -17.106 1.00 38.73 O +ATOM 530 CB LEU B 16 38.245 -21.104 -15.143 1.00 44.15 C +ATOM 531 CG LEU B 16 37.708 -22.399 -14.535 1.00 48.75 C +ATOM 532 CD1 LEU B 16 38.687 -22.946 -13.495 1.00 49.57 C +ATOM 533 CD2 LEU B 16 36.357 -22.110 -13.881 1.00 50.44 C +ATOM 534 N ASP B 17 39.215 -21.254 -18.185 1.00 42.91 N +ATOM 535 CA ASP B 17 39.165 -21.894 -19.502 1.00 44.31 C +ATOM 536 C ASP B 17 40.559 -22.276 -19.972 1.00 42.53 C +ATOM 537 O ASP B 17 40.769 -23.351 -20.514 1.00 41.07 O +ATOM 538 CB ASP B 17 38.549 -20.959 -20.545 1.00 49.28 C +ATOM 539 CG ASP B 17 37.127 -21.341 -20.904 1.00 55.95 C +ATOM 540 OD1 ASP B 17 36.194 -20.637 -20.463 1.00 59.05 O +ATOM 541 OD2 ASP B 17 36.944 -22.349 -21.625 1.00 59.32 O +ATOM 542 N ARG B 18 41.504 -21.371 -19.772 1.00 41.08 N +ATOM 543 CA ARG B 18 42.878 -21.599 -20.165 1.00 42.67 C +ATOM 544 C ARG B 18 43.502 -22.756 -19.370 1.00 42.93 C +ATOM 545 O ARG B 18 44.212 -23.592 -19.939 1.00 43.96 O +ATOM 546 CB ARG B 18 43.669 -20.308 -19.971 1.00 45.53 C +ATOM 547 CG ARG B 18 45.081 -20.330 -20.506 1.00 50.58 C +ATOM 548 CD ARG B 18 45.579 -18.905 -20.650 1.00 53.74 C +ATOM 549 NE ARG B 18 45.398 -18.154 -19.413 1.00 58.54 N +ATOM 550 CZ ARG B 18 45.445 -16.829 -19.325 1.00 60.56 C +ATOM 551 NH1 ARG B 18 45.667 -16.095 -20.408 1.00 62.08 N +ATOM 552 NH2 ARG B 18 45.268 -16.237 -18.151 1.00 62.24 N +ATOM 553 N LEU B 19 43.241 -22.819 -18.065 1.00 39.07 N +ATOM 554 CA LEU B 19 43.791 -23.909 -17.254 1.00 38.36 C +ATOM 555 C LEU B 19 43.215 -25.255 -17.699 1.00 39.30 C +ATOM 556 O LEU B 19 43.950 -26.236 -17.850 1.00 36.37 O +ATOM 557 CB LEU B 19 43.490 -23.705 -15.762 1.00 36.35 C +ATOM 558 CG LEU B 19 44.286 -22.626 -15.012 1.00 38.72 C +ATOM 559 CD1 LEU B 19 43.634 -22.346 -13.657 1.00 37.63 C +ATOM 560 CD2 LEU B 19 45.724 -23.073 -14.836 1.00 37.76 C +ATOM 561 N LYS B 20 41.902 -25.305 -17.899 1.00 35.91 N +ATOM 562 CA LYS B 20 41.270 -26.547 -18.324 1.00 38.58 C +ATOM 563 C LYS B 20 41.811 -26.989 -19.687 1.00 38.13 C +ATOM 564 O LYS B 20 41.978 -28.174 -19.956 1.00 36.11 O +ATOM 565 CB LYS B 20 39.756 -26.375 -18.403 1.00 37.92 C +ATOM 566 CG LYS B 20 39.033 -27.676 -18.661 1.00 44.30 C +ATOM 567 CD LYS B 20 37.529 -27.537 -18.472 1.00 46.19 C +ATOM 568 CE LYS B 20 36.846 -28.880 -18.640 1.00 50.92 C +ATOM 569 NZ LYS B 20 35.386 -28.796 -18.375 1.00 54.82 N +ATOM 570 N MET B 21 42.069 -26.014 -20.546 1.00 38.48 N +ATOM 571 CA MET B 21 42.598 -26.271 -21.872 1.00 40.36 C +ATOM 572 C MET B 21 43.992 -26.928 -21.780 1.00 40.20 C +ATOM 573 O MET B 21 44.271 -27.918 -22.459 1.00 38.73 O +ATOM 574 CB MET B 21 42.669 -24.942 -22.632 1.00 43.78 C +ATOM 575 CG MET B 21 43.136 -25.043 -24.064 1.00 51.54 C +ATOM 576 SD MET B 21 43.198 -23.435 -24.857 1.00 60.61 S +ATOM 577 CE MET B 21 44.872 -22.924 -24.432 1.00 58.00 C +ATOM 578 N LYS B 22 44.858 -26.377 -20.936 1.00 38.34 N +ATOM 579 CA LYS B 22 46.207 -26.908 -20.768 1.00 39.76 C +ATOM 580 C LYS B 22 46.174 -28.318 -20.168 1.00 40.85 C +ATOM 581 O LYS B 22 47.009 -29.167 -20.508 1.00 36.90 O +ATOM 582 CB LYS B 22 47.036 -25.984 -19.873 1.00 40.40 C +ATOM 583 CG LYS B 22 47.146 -24.554 -20.390 1.00 46.57 C +ATOM 584 CD LYS B 22 48.399 -24.309 -21.208 1.00 52.69 C +ATOM 585 CE LYS B 22 48.495 -25.212 -22.432 1.00 58.88 C +ATOM 586 NZ LYS B 22 49.727 -24.908 -23.238 1.00 61.66 N +ATOM 587 N LEU B 23 45.213 -28.564 -19.281 1.00 37.43 N +ATOM 588 CA LEU B 23 45.088 -29.875 -18.666 1.00 39.23 C +ATOM 589 C LEU B 23 44.824 -30.945 -19.725 1.00 40.12 C +ATOM 590 O LEU B 23 45.404 -32.041 -19.665 1.00 40.57 O +ATOM 591 CB LEU B 23 43.974 -29.872 -17.615 1.00 37.34 C +ATOM 592 CG LEU B 23 44.300 -29.102 -16.329 1.00 39.75 C +ATOM 593 CD1 LEU B 23 43.056 -29.031 -15.420 1.00 37.82 C +ATOM 594 CD2 LEU B 23 45.461 -29.782 -15.612 1.00 38.12 C +ATOM 595 N GLN B 24 43.960 -30.634 -20.691 1.00 38.82 N +ATOM 596 CA GLN B 24 43.650 -31.580 -21.762 1.00 40.43 C +ATOM 597 C GLN B 24 44.925 -31.939 -22.544 1.00 41.00 C +ATOM 598 O GLN B 24 45.149 -33.105 -22.863 1.00 37.73 O +ATOM 599 CB GLN B 24 42.621 -30.999 -22.742 1.00 43.30 C +ATOM 600 CG GLN B 24 41.374 -30.407 -22.094 1.00 46.05 C +ATOM 601 CD GLN B 24 40.798 -31.303 -21.024 1.00 47.81 C +ATOM 602 OE1 GLN B 24 40.284 -32.378 -21.316 1.00 48.26 O +ATOM 603 NE2 GLN B 24 40.889 -30.865 -19.768 1.00 47.94 N +ATOM 604 N GLU B 25 45.752 -30.937 -22.844 1.00 40.38 N +ATOM 605 CA GLU B 25 46.997 -31.162 -23.584 1.00 42.86 C +ATOM 606 C GLU B 25 47.955 -32.073 -22.832 1.00 42.71 C +ATOM 607 O GLU B 25 48.772 -32.751 -23.452 1.00 45.23 O +ATOM 608 CB GLU B 25 47.719 -29.839 -23.873 1.00 43.17 C +ATOM 609 CG GLU B 25 46.916 -28.845 -24.692 1.00 45.39 C +ATOM 610 CD GLU B 25 47.671 -27.546 -24.940 1.00 48.00 C +ATOM 611 OE1 GLU B 25 47.086 -26.617 -25.532 1.00 46.97 O +ATOM 612 OE2 GLU B 25 48.852 -27.453 -24.547 1.00 48.19 O +ATOM 613 N LYS B 26 47.872 -32.082 -21.503 1.00 42.37 N +ATOM 614 CA LYS B 26 48.758 -32.917 -20.691 1.00 41.49 C +ATOM 615 C LYS B 26 48.124 -34.260 -20.344 1.00 41.33 C +ATOM 616 O LYS B 26 48.668 -35.027 -19.551 1.00 39.86 O +ATOM 617 CB LYS B 26 49.140 -32.195 -19.396 1.00 43.97 C +ATOM 618 CG LYS B 26 49.781 -30.833 -19.599 1.00 47.94 C +ATOM 619 CD LYS B 26 50.953 -30.893 -20.567 1.00 49.98 C +ATOM 620 CE LYS B 26 51.521 -29.504 -20.800 1.00 52.92 C +ATOM 621 NZ LYS B 26 52.544 -29.476 -21.876 1.00 54.14 N +ATOM 622 N GLY B 27 46.966 -34.538 -20.928 1.00 41.50 N +ATOM 623 CA GLY B 27 46.302 -35.797 -20.656 1.00 40.92 C +ATOM 624 C GLY B 27 45.760 -35.943 -19.248 1.00 42.77 C +ATOM 625 O GLY B 27 45.492 -37.063 -18.813 1.00 43.42 O +ATOM 626 N ASP B 28 45.611 -34.834 -18.521 1.00 43.17 N +ATOM 627 CA ASP B 28 45.069 -34.890 -17.163 1.00 44.14 C +ATOM 628 C ASP B 28 43.606 -34.449 -17.187 1.00 46.30 C +ATOM 629 O ASP B 28 43.300 -33.256 -17.091 1.00 44.84 O +ATOM 630 CB ASP B 28 45.849 -33.987 -16.214 1.00 44.37 C +ATOM 631 CG ASP B 28 45.321 -34.054 -14.797 1.00 47.08 C +ATOM 632 OD1 ASP B 28 45.871 -33.372 -13.901 1.00 45.91 O +ATOM 633 OD2 ASP B 28 44.345 -34.804 -14.579 1.00 49.31 O +ATOM 634 N THR B 29 42.708 -35.420 -17.317 1.00 46.90 N +ATOM 635 CA THR B 29 41.278 -35.138 -17.377 1.00 47.45 C +ATOM 636 C THR B 29 40.559 -35.369 -16.051 1.00 46.64 C +ATOM 637 O THR B 29 39.336 -35.261 -15.985 1.00 47.05 O +ATOM 638 CB THR B 29 40.597 -36.017 -18.447 1.00 47.53 C +ATOM 639 OG1 THR B 29 40.807 -37.398 -18.129 1.00 48.52 O +ATOM 640 CG2 THR B 29 41.169 -35.728 -19.828 1.00 49.88 C +ATOM 641 N SER B 30 41.323 -35.664 -15.001 1.00 45.13 N +ATOM 642 CA SER B 30 40.778 -35.953 -13.679 1.00 45.00 C +ATOM 643 C SER B 30 39.989 -34.840 -12.988 1.00 47.50 C +ATOM 644 O SER B 30 39.181 -35.117 -12.102 1.00 46.64 O +ATOM 645 CB SER B 30 41.900 -36.392 -12.740 1.00 43.95 C +ATOM 646 OG SER B 30 42.770 -35.309 -12.431 1.00 43.80 O +ATOM 647 N GLN B 31 40.227 -33.587 -13.366 1.00 48.03 N +ATOM 648 CA GLN B 31 39.524 -32.481 -12.726 1.00 47.58 C +ATOM 649 C GLN B 31 38.463 -31.871 -13.633 1.00 47.77 C +ATOM 650 O GLN B 31 37.864 -30.855 -13.286 1.00 48.57 O +ATOM 651 CB GLN B 31 40.516 -31.383 -12.327 1.00 49.53 C +ATOM 652 CG GLN B 31 41.702 -31.840 -11.489 1.00 51.22 C +ATOM 653 CD GLN B 31 41.284 -32.513 -10.199 1.00 55.69 C +ATOM 654 OE1 GLN B 31 40.454 -31.990 -9.454 1.00 56.04 O +ATOM 655 NE2 GLN B 31 41.867 -33.676 -9.920 1.00 55.29 N +ATOM 656 N ASN B 32 38.228 -32.484 -14.790 1.00 46.81 N +ATOM 657 CA ASN B 32 37.257 -31.951 -15.745 1.00 47.72 C +ATOM 658 C ASN B 32 35.842 -31.706 -15.214 1.00 48.83 C +ATOM 659 O ASN B 32 35.228 -30.685 -15.533 1.00 44.64 O +ATOM 660 CB ASN B 32 37.201 -32.845 -16.977 1.00 47.63 C +ATOM 661 CG ASN B 32 38.336 -32.561 -17.944 1.00 48.34 C +ATOM 662 OD1 ASN B 32 39.359 -31.984 -17.569 1.00 48.76 O +ATOM 663 ND2 ASN B 32 38.168 -32.975 -19.188 1.00 47.07 N +ATOM 664 N GLU B 33 35.334 -32.638 -14.413 1.00 50.55 N +ATOM 665 CA GLU B 33 34.002 -32.519 -13.834 1.00 54.33 C +ATOM 666 C GLU B 33 33.961 -31.361 -12.845 1.00 53.25 C +ATOM 667 O GLU B 33 33.097 -30.485 -12.932 1.00 53.61 O +ATOM 668 CB GLU B 33 33.621 -33.817 -13.117 1.00 58.79 C +ATOM 669 CG GLU B 33 33.543 -35.031 -14.029 1.00 66.24 C +ATOM 670 CD GLU B 33 33.634 -36.345 -13.260 1.00 71.89 C +ATOM 671 OE1 GLU B 33 32.789 -36.571 -12.363 1.00 72.86 O +ATOM 672 OE2 GLU B 33 34.554 -37.150 -13.552 1.00 74.62 O +ATOM 673 N LYS B 34 34.900 -31.355 -11.906 1.00 51.72 N +ATOM 674 CA LYS B 34 34.955 -30.298 -10.908 1.00 52.11 C +ATOM 675 C LYS B 34 35.169 -28.920 -11.527 1.00 49.74 C +ATOM 676 O LYS B 34 34.600 -27.939 -11.065 1.00 49.65 O +ATOM 677 CB LYS B 34 36.059 -30.580 -9.887 1.00 54.44 C +ATOM 678 CG LYS B 34 35.808 -31.825 -9.046 1.00 59.48 C +ATOM 679 CD LYS B 34 36.847 -31.966 -7.943 1.00 61.96 C +ATOM 680 CE LYS B 34 36.601 -33.224 -7.125 1.00 64.33 C +ATOM 681 NZ LYS B 34 36.659 -34.445 -7.986 1.00 66.85 N +ATOM 682 N LEU B 35 35.993 -28.840 -12.564 1.00 46.14 N +ATOM 683 CA LEU B 35 36.239 -27.559 -13.208 1.00 45.72 C +ATOM 684 C LEU B 35 34.993 -27.100 -13.955 1.00 44.24 C +ATOM 685 O LEU B 35 34.680 -25.912 -13.979 1.00 41.82 O +ATOM 686 CB LEU B 35 37.421 -27.654 -14.173 1.00 44.26 C +ATOM 687 CG LEU B 35 38.795 -27.774 -13.510 1.00 45.34 C +ATOM 688 CD1 LEU B 35 39.864 -27.895 -14.588 1.00 43.12 C +ATOM 689 CD2 LEU B 35 39.060 -26.560 -12.628 1.00 45.00 C +ATOM 690 N SER B 36 34.289 -28.050 -14.564 1.00 43.92 N +ATOM 691 CA SER B 36 33.070 -27.739 -15.291 1.00 46.53 C +ATOM 692 C SER B 36 32.017 -27.185 -14.331 1.00 47.43 C +ATOM 693 O SER B 36 31.304 -26.243 -14.662 1.00 46.68 O +ATOM 694 CB SER B 36 32.525 -28.988 -15.989 1.00 46.83 C +ATOM 695 OG SER B 36 33.254 -29.270 -17.173 1.00 50.63 O +ATOM 696 N MET B 37 31.926 -27.771 -13.144 1.00 47.43 N +ATOM 697 CA MET B 37 30.955 -27.311 -12.166 1.00 50.97 C +ATOM 698 C MET B 37 31.365 -25.936 -11.648 1.00 50.01 C +ATOM 699 O MET B 37 30.533 -25.040 -11.509 1.00 49.09 O +ATOM 700 CB MET B 37 30.846 -28.306 -11.007 1.00 55.75 C +ATOM 701 CG MET B 37 30.439 -29.712 -11.436 1.00 62.12 C +ATOM 702 SD MET B 37 29.880 -30.749 -10.060 1.00 71.88 S +ATOM 703 CE MET B 37 31.332 -30.698 -8.966 1.00 69.43 C +ATOM 704 N PHE B 38 32.653 -25.768 -11.381 1.00 46.67 N +ATOM 705 CA PHE B 38 33.162 -24.499 -10.884 1.00 45.81 C +ATOM 706 C PHE B 38 32.839 -23.406 -11.905 1.00 44.36 C +ATOM 707 O PHE B 38 32.432 -22.303 -11.539 1.00 43.77 O +ATOM 708 CB PHE B 38 34.673 -24.614 -10.639 1.00 45.02 C +ATOM 709 CG PHE B 38 35.294 -23.400 -9.996 1.00 46.47 C +ATOM 710 CD1 PHE B 38 34.573 -22.611 -9.106 1.00 47.00 C +ATOM 711 CD2 PHE B 38 36.621 -23.072 -10.251 1.00 45.91 C +ATOM 712 CE1 PHE B 38 35.166 -21.512 -8.477 1.00 47.15 C +ATOM 713 CE2 PHE B 38 37.223 -21.979 -9.629 1.00 48.52 C +ATOM 714 CZ PHE B 38 36.493 -21.196 -8.740 1.00 47.25 C +ATOM 715 N TYR B 39 33.004 -23.732 -13.185 1.00 43.67 N +ATOM 716 CA TYR B 39 32.727 -22.805 -14.288 1.00 43.36 C +ATOM 717 C TYR B 39 31.237 -22.432 -14.342 1.00 44.56 C +ATOM 718 O TYR B 39 30.877 -21.270 -14.514 1.00 41.54 O +ATOM 719 CB TYR B 39 33.097 -23.451 -15.624 1.00 43.76 C +ATOM 720 CG TYR B 39 33.153 -22.484 -16.779 1.00 44.25 C +ATOM 721 CD1 TYR B 39 34.271 -21.679 -16.976 1.00 45.12 C +ATOM 722 CD2 TYR B 39 32.093 -22.370 -17.675 1.00 46.21 C +ATOM 723 CE1 TYR B 39 34.342 -20.782 -18.036 1.00 45.84 C +ATOM 724 CE2 TYR B 39 32.150 -21.470 -18.750 1.00 47.55 C +ATOM 725 CZ TYR B 39 33.282 -20.681 -18.919 1.00 47.42 C +ATOM 726 OH TYR B 39 33.368 -19.788 -19.965 1.00 48.84 O +ATOM 727 N GLU B 40 30.382 -23.442 -14.235 1.00 45.13 N +ATOM 728 CA GLU B 40 28.946 -23.230 -14.269 1.00 49.24 C +ATOM 729 C GLU B 40 28.529 -22.259 -13.165 1.00 48.82 C +ATOM 730 O GLU B 40 27.751 -21.333 -13.404 1.00 48.01 O +ATOM 731 CB GLU B 40 28.209 -24.558 -14.092 1.00 51.45 C +ATOM 732 CG GLU B 40 28.351 -25.517 -15.260 1.00 61.40 C +ATOM 733 CD GLU B 40 27.742 -26.881 -14.959 1.00 68.15 C +ATOM 734 OE1 GLU B 40 26.523 -26.936 -14.681 1.00 72.51 O +ATOM 735 OE2 GLU B 40 28.482 -27.895 -14.991 1.00 71.28 O +ATOM 736 N THR B 41 29.056 -22.459 -11.962 1.00 46.59 N +ATOM 737 CA THR B 41 28.706 -21.583 -10.858 1.00 46.18 C +ATOM 738 C THR B 41 29.160 -20.149 -11.125 1.00 45.60 C +ATOM 739 O THR B 41 28.375 -19.217 -10.990 1.00 44.45 O +ATOM 740 CB THR B 41 29.310 -22.082 -9.524 1.00 45.74 C +ATOM 741 OG1 THR B 41 28.833 -23.403 -9.250 1.00 45.79 O +ATOM 742 CG2 THR B 41 28.890 -21.171 -8.373 1.00 48.00 C +ATOM 743 N LEU B 42 30.416 -19.973 -11.522 1.00 44.60 N +ATOM 744 CA LEU B 42 30.946 -18.640 -11.793 1.00 45.27 C +ATOM 745 C LEU B 42 30.252 -17.932 -12.944 1.00 45.76 C +ATOM 746 O LEU B 42 30.348 -16.712 -13.080 1.00 44.50 O +ATOM 747 CB LEU B 42 32.441 -18.710 -12.096 1.00 46.98 C +ATOM 748 CG LEU B 42 33.381 -18.944 -10.910 1.00 49.87 C +ATOM 749 CD1 LEU B 42 34.785 -19.237 -11.419 1.00 49.85 C +ATOM 750 CD2 LEU B 42 33.376 -17.718 -10.006 1.00 49.27 C +ATOM 751 N LYS B 43 29.553 -18.694 -13.773 1.00 45.39 N +ATOM 752 CA LYS B 43 28.874 -18.116 -14.923 1.00 48.46 C +ATOM 753 C LYS B 43 27.388 -17.826 -14.682 1.00 47.42 C +ATOM 754 O LYS B 43 26.760 -17.092 -15.443 1.00 48.19 O +ATOM 755 CB LYS B 43 29.015 -19.059 -16.122 1.00 48.81 C +ATOM 756 CG LYS B 43 28.770 -18.396 -17.454 1.00 55.53 C +ATOM 757 CD LYS B 43 28.948 -19.373 -18.605 1.00 60.98 C +ATOM 758 CE LYS B 43 28.860 -18.653 -19.950 1.00 63.58 C +ATOM 759 NZ LYS B 43 29.886 -17.567 -20.076 1.00 64.09 N +ATOM 760 N SER B 44 26.826 -18.398 -13.626 1.00 45.59 N +ATOM 761 CA SER B 44 25.411 -18.212 -13.348 1.00 46.52 C +ATOM 762 C SER B 44 25.043 -16.809 -12.874 1.00 44.72 C +ATOM 763 O SER B 44 25.730 -16.210 -12.049 1.00 43.79 O +ATOM 764 CB SER B 44 24.956 -19.224 -12.315 1.00 45.46 C +ATOM 765 OG SER B 44 25.573 -18.948 -11.082 1.00 51.46 O +ATOM 766 N PRO B 45 23.955 -16.253 -13.419 1.00 46.80 N +ATOM 767 CA PRO B 45 23.522 -14.908 -13.015 1.00 45.23 C +ATOM 768 C PRO B 45 23.218 -14.817 -11.523 1.00 44.36 C +ATOM 769 O PRO B 45 23.572 -13.840 -10.865 1.00 45.49 O +ATOM 770 CB PRO B 45 22.296 -14.653 -13.898 1.00 46.86 C +ATOM 771 CG PRO B 45 21.851 -16.029 -14.325 1.00 48.62 C +ATOM 772 CD PRO B 45 23.149 -16.752 -14.545 1.00 47.46 C +ATOM 773 N LEU B 46 22.588 -15.847 -10.972 1.00 44.65 N +ATOM 774 CA LEU B 46 22.271 -15.834 -9.550 1.00 44.38 C +ATOM 775 C LEU B 46 23.531 -15.696 -8.706 1.00 44.60 C +ATOM 776 O LEU B 46 23.600 -14.857 -7.813 1.00 46.13 O +ATOM 777 CB LEU B 46 21.535 -17.108 -9.128 1.00 44.53 C +ATOM 778 CG LEU B 46 21.200 -17.076 -7.628 1.00 48.15 C +ATOM 779 CD1 LEU B 46 20.128 -16.016 -7.387 1.00 46.24 C +ATOM 780 CD2 LEU B 46 20.717 -18.438 -7.141 1.00 50.19 C +ATOM 781 N PHE B 47 24.529 -16.528 -8.982 1.00 43.75 N +ATOM 782 CA PHE B 47 25.775 -16.481 -8.227 1.00 41.27 C +ATOM 783 C PHE B 47 26.455 -15.115 -8.324 1.00 39.55 C +ATOM 784 O PHE B 47 26.984 -14.600 -7.344 1.00 41.07 O +ATOM 785 CB PHE B 47 26.748 -17.557 -8.732 1.00 40.32 C +ATOM 786 CG PHE B 47 28.112 -17.455 -8.123 1.00 39.71 C +ATOM 787 CD1 PHE B 47 28.375 -18.012 -6.875 1.00 39.43 C +ATOM 788 CD2 PHE B 47 29.123 -16.759 -8.776 1.00 37.02 C +ATOM 789 CE1 PHE B 47 29.628 -17.877 -6.282 1.00 41.05 C +ATOM 790 CE2 PHE B 47 30.386 -16.613 -8.191 1.00 41.15 C +ATOM 791 CZ PHE B 47 30.639 -17.173 -6.943 1.00 39.81 C +ATOM 792 N ASN B 48 26.461 -14.540 -9.517 1.00 38.54 N +ATOM 793 CA ASN B 48 27.100 -13.248 -9.713 1.00 40.10 C +ATOM 794 C ASN B 48 26.390 -12.134 -8.952 1.00 40.29 C +ATOM 795 O ASN B 48 27.026 -11.193 -8.475 1.00 40.45 O +ATOM 796 CB ASN B 48 27.172 -12.935 -11.205 1.00 38.72 C +ATOM 797 CG ASN B 48 28.368 -13.606 -11.882 1.00 41.13 C +ATOM 798 OD1 ASN B 48 29.461 -13.048 -11.915 1.00 38.78 O +ATOM 799 ND2 ASN B 48 28.162 -14.813 -12.400 1.00 34.92 N +ATOM 800 N GLN B 49 25.071 -12.244 -8.833 1.00 39.97 N +ATOM 801 CA GLN B 49 24.297 -11.243 -8.099 1.00 38.84 C +ATOM 802 C GLN B 49 24.642 -11.354 -6.618 1.00 37.07 C +ATOM 803 O GLN B 49 24.924 -10.360 -5.950 1.00 36.67 O +ATOM 804 CB GLN B 49 22.799 -11.481 -8.320 1.00 38.65 C +ATOM 805 CG GLN B 49 22.314 -11.106 -9.718 1.00 40.78 C +ATOM 806 CD GLN B 49 20.907 -11.615 -10.009 1.00 48.08 C +ATOM 807 OE1 GLN B 49 20.090 -11.767 -9.102 1.00 49.87 O +ATOM 808 NE2 GLN B 49 20.615 -11.862 -11.280 1.00 50.57 N +ATOM 809 N ILE B 50 24.639 -12.581 -6.113 1.00 37.87 N +ATOM 810 CA ILE B 50 24.946 -12.832 -4.718 1.00 38.45 C +ATOM 811 C ILE B 50 26.359 -12.392 -4.352 1.00 39.72 C +ATOM 812 O ILE B 50 26.582 -11.817 -3.286 1.00 38.36 O +ATOM 813 CB ILE B 50 24.782 -14.326 -4.391 1.00 41.48 C +ATOM 814 CG1 ILE B 50 23.317 -14.733 -4.574 1.00 40.90 C +ATOM 815 CG2 ILE B 50 25.267 -14.605 -2.975 1.00 40.19 C +ATOM 816 CD1 ILE B 50 23.072 -16.226 -4.434 1.00 45.56 C +ATOM 817 N LEU B 51 27.314 -12.670 -5.235 1.00 39.95 N +ATOM 818 CA LEU B 51 28.709 -12.306 -4.990 1.00 39.67 C +ATOM 819 C LEU B 51 28.848 -10.795 -4.945 1.00 38.47 C +ATOM 820 O LEU B 51 29.473 -10.251 -4.045 1.00 39.76 O +ATOM 821 CB LEU B 51 29.614 -12.879 -6.090 1.00 40.92 C +ATOM 822 CG LEU B 51 31.120 -12.616 -5.971 1.00 43.72 C +ATOM 823 CD1 LEU B 51 31.675 -13.274 -4.717 1.00 45.29 C +ATOM 824 CD2 LEU B 51 31.825 -13.161 -7.214 1.00 46.96 C +ATOM 825 N THR B 52 28.258 -10.114 -5.916 1.00 37.93 N +ATOM 826 CA THR B 52 28.333 -8.663 -5.954 1.00 39.24 C +ATOM 827 C THR B 52 27.758 -8.051 -4.664 1.00 41.40 C +ATOM 828 O THR B 52 28.362 -7.152 -4.069 1.00 40.80 O +ATOM 829 CB THR B 52 27.554 -8.111 -7.158 1.00 39.79 C +ATOM 830 OG1 THR B 52 28.084 -8.674 -8.362 1.00 40.02 O +ATOM 831 CG2 THR B 52 27.660 -6.585 -7.219 1.00 39.14 C +ATOM 832 N LEU B 53 26.598 -8.539 -4.229 1.00 40.09 N +ATOM 833 CA LEU B 53 25.979 -8.004 -3.021 1.00 43.20 C +ATOM 834 C LEU B 53 26.827 -8.333 -1.812 1.00 43.20 C +ATOM 835 O LEU B 53 26.952 -7.527 -0.885 1.00 41.39 O +ATOM 836 CB LEU B 53 24.571 -8.572 -2.833 1.00 44.53 C +ATOM 837 CG LEU B 53 23.428 -7.728 -3.397 1.00 49.42 C +ATOM 838 CD1 LEU B 53 22.121 -8.495 -3.255 1.00 50.72 C +ATOM 839 CD2 LEU B 53 23.351 -6.398 -2.654 1.00 48.00 C +ATOM 840 N GLN B 54 27.400 -9.532 -1.832 1.00 44.04 N +ATOM 841 CA GLN B 54 28.268 -10.004 -0.760 1.00 46.31 C +ATOM 842 C GLN B 54 29.437 -9.023 -0.577 1.00 44.89 C +ATOM 843 O GLN B 54 29.785 -8.668 0.550 1.00 45.40 O +ATOM 844 CB GLN B 54 28.805 -11.392 -1.122 1.00 50.71 C +ATOM 845 CG GLN B 54 28.894 -12.370 0.016 1.00 56.81 C +ATOM 846 CD GLN B 54 27.531 -12.741 0.565 1.00 60.41 C +ATOM 847 OE1 GLN B 54 26.909 -11.966 1.285 1.00 60.36 O +ATOM 848 NE2 GLN B 54 27.056 -13.931 0.215 1.00 63.57 N +ATOM 849 N GLN B 55 30.026 -8.575 -1.687 1.00 43.54 N +ATOM 850 CA GLN B 55 31.158 -7.639 -1.635 1.00 44.92 C +ATOM 851 C GLN B 55 30.707 -6.245 -1.197 1.00 42.39 C +ATOM 852 O GLN B 55 31.430 -5.538 -0.497 1.00 43.47 O +ATOM 853 CB GLN B 55 31.839 -7.544 -3.006 1.00 47.68 C +ATOM 854 CG GLN B 55 33.366 -7.762 -3.003 1.00 56.74 C +ATOM 855 CD GLN B 55 34.142 -6.758 -2.153 1.00 59.44 C +ATOM 856 OE1 GLN B 55 34.385 -6.986 -0.965 1.00 60.78 O +ATOM 857 NE2 GLN B 55 34.531 -5.638 -2.764 1.00 60.29 N +ATOM 858 N SER B 56 29.514 -5.842 -1.618 1.00 39.14 N +ATOM 859 CA SER B 56 28.989 -4.530 -1.237 1.00 37.88 C +ATOM 860 C SER B 56 28.816 -4.473 0.271 1.00 36.40 C +ATOM 861 O SER B 56 29.108 -3.457 0.912 1.00 35.53 O +ATOM 862 CB SER B 56 27.649 -4.275 -1.920 1.00 35.79 C +ATOM 863 OG SER B 56 27.830 -4.142 -3.318 1.00 34.54 O +ATOM 864 N ILE B 57 28.356 -5.584 0.833 1.00 36.34 N +ATOM 865 CA ILE B 57 28.142 -5.670 2.266 1.00 38.67 C +ATOM 866 C ILE B 57 29.483 -5.620 2.992 1.00 41.10 C +ATOM 867 O ILE B 57 29.627 -4.901 3.981 1.00 40.38 O +ATOM 868 CB ILE B 57 27.360 -6.959 2.629 1.00 38.47 C +ATOM 869 CG1 ILE B 57 25.915 -6.829 2.120 1.00 36.85 C +ATOM 870 CG2 ILE B 57 27.366 -7.191 4.135 1.00 36.60 C +ATOM 871 CD1 ILE B 57 25.078 -8.078 2.282 1.00 34.70 C +ATOM 872 N LYS B 58 30.467 -6.362 2.487 1.00 42.84 N +ATOM 873 CA LYS B 58 31.792 -6.365 3.105 1.00 44.29 C +ATOM 874 C LYS B 58 32.323 -4.932 3.080 1.00 42.72 C +ATOM 875 O LYS B 58 32.841 -4.421 4.068 1.00 43.58 O +ATOM 876 CB LYS B 58 32.743 -7.282 2.333 1.00 47.03 C +ATOM 877 CG LYS B 58 34.099 -7.429 2.998 1.00 51.35 C +ATOM 878 CD LYS B 58 33.960 -8.120 4.351 1.00 55.95 C +ATOM 879 CE LYS B 58 34.727 -7.390 5.456 1.00 60.25 C +ATOM 880 NZ LYS B 58 34.157 -6.038 5.772 1.00 60.30 N +ATOM 881 N GLN B 59 32.169 -4.284 1.939 1.00 42.54 N +ATOM 882 CA GLN B 59 32.620 -2.914 1.782 1.00 44.60 C +ATOM 883 C GLN B 59 32.011 -2.000 2.859 1.00 44.68 C +ATOM 884 O GLN B 59 32.730 -1.264 3.545 1.00 44.17 O +ATOM 885 CB GLN B 59 32.223 -2.409 0.400 1.00 50.13 C +ATOM 886 CG GLN B 59 33.238 -1.487 -0.230 1.00 59.31 C +ATOM 887 CD GLN B 59 34.392 -2.250 -0.831 1.00 61.14 C +ATOM 888 OE1 GLN B 59 34.246 -2.899 -1.866 1.00 63.57 O +ATOM 889 NE2 GLN B 59 35.547 -2.192 -0.179 1.00 64.31 N +ATOM 890 N LEU B 60 30.688 -2.046 3.021 1.00 41.22 N +ATOM 891 CA LEU B 60 30.052 -1.184 4.014 1.00 40.50 C +ATOM 892 C LEU B 60 30.439 -1.579 5.434 1.00 40.01 C +ATOM 893 O LEU B 60 30.608 -0.716 6.288 1.00 37.63 O +ATOM 894 CB LEU B 60 28.524 -1.176 3.842 1.00 39.34 C +ATOM 895 CG LEU B 60 28.037 -0.630 2.491 1.00 40.63 C +ATOM 896 CD1 LEU B 60 26.633 -0.076 2.640 1.00 43.87 C +ATOM 897 CD2 LEU B 60 28.967 0.480 2.004 1.00 43.08 C +ATOM 898 N LYS B 61 30.578 -2.874 5.689 1.00 41.14 N +ATOM 899 CA LYS B 61 30.987 -3.331 7.018 1.00 45.53 C +ATOM 900 C LYS B 61 32.399 -2.805 7.305 1.00 45.98 C +ATOM 901 O LYS B 61 32.706 -2.394 8.423 1.00 46.13 O +ATOM 902 CB LYS B 61 30.980 -4.861 7.088 1.00 46.77 C +ATOM 903 CG LYS B 61 29.605 -5.461 7.317 1.00 49.70 C +ATOM 904 CD LYS B 61 29.687 -6.974 7.409 1.00 52.40 C +ATOM 905 CE LYS B 61 28.342 -7.574 7.761 1.00 53.79 C +ATOM 906 NZ LYS B 61 28.395 -9.064 7.799 1.00 56.54 N +ATOM 907 N GLY B 62 33.246 -2.819 6.278 1.00 47.35 N +ATOM 908 CA GLY B 62 34.600 -2.317 6.425 1.00 47.23 C +ATOM 909 C GLY B 62 34.538 -0.837 6.737 1.00 46.72 C +ATOM 910 O GLY B 62 35.358 -0.321 7.487 1.00 47.97 O +ATOM 911 N GLN B 63 33.551 -0.152 6.169 1.00 46.18 N +ATOM 912 CA GLN B 63 33.371 1.275 6.417 1.00 45.43 C +ATOM 913 C GLN B 63 32.966 1.477 7.874 1.00 46.62 C +ATOM 914 O GLN B 63 33.432 2.408 8.546 1.00 45.65 O +ATOM 915 CB GLN B 63 32.285 1.834 5.509 1.00 43.44 C +ATOM 916 CG GLN B 63 32.102 3.329 5.607 1.00 40.98 C +ATOM 917 CD GLN B 63 30.887 3.806 4.825 1.00 40.00 C +ATOM 918 OE1 GLN B 63 30.435 3.138 3.897 1.00 37.16 O +ATOM 919 NE2 GLN B 63 30.367 4.972 5.185 1.00 38.20 N +ATOM 920 N LEU B 64 32.094 0.600 8.361 1.00 46.26 N +ATOM 921 CA LEU B 64 31.648 0.683 9.744 1.00 47.42 C +ATOM 922 C LEU B 64 32.842 0.453 10.681 1.00 48.45 C +ATOM 923 O LEU B 64 33.023 1.195 11.648 1.00 45.64 O +ATOM 924 CB LEU B 64 30.556 -0.355 10.016 1.00 46.52 C +ATOM 925 CG LEU B 64 30.001 -0.418 11.444 1.00 47.74 C +ATOM 926 CD1 LEU B 64 29.622 0.975 11.925 1.00 47.48 C +ATOM 927 CD2 LEU B 64 28.792 -1.352 11.474 1.00 47.81 C +ATOM 928 N ASN B 65 33.644 -0.572 10.387 1.00 50.67 N +ATOM 929 CA ASN B 65 34.830 -0.884 11.191 1.00 54.95 C +ATOM 930 C ASN B 65 35.715 0.344 11.349 1.00 55.46 C +ATOM 931 O ASN B 65 36.188 0.628 12.440 1.00 56.56 O +ATOM 932 CB ASN B 65 35.663 -2.000 10.553 1.00 57.35 C +ATOM 933 CG ASN B 65 35.099 -3.378 10.815 1.00 61.15 C +ATOM 934 OD1 ASN B 65 34.671 -3.679 11.929 1.00 65.37 O +ATOM 935 ND2 ASN B 65 35.111 -4.234 9.793 1.00 62.40 N +ATOM 936 N HIS B 66 35.942 1.066 10.257 1.00 56.12 N +ATOM 937 CA HIS B 66 36.768 2.262 10.312 1.00 59.59 C +ATOM 938 C HIS B 66 36.156 3.358 11.178 1.00 60.36 C +ATOM 939 O HIS B 66 36.877 4.126 11.820 1.00 59.98 O +ATOM 940 CB HIS B 66 37.018 2.805 8.906 1.00 62.92 C +ATOM 941 CG HIS B 66 38.074 2.059 8.154 1.00 69.29 C +ATOM 942 ND1 HIS B 66 39.317 1.791 8.690 1.00 71.55 N +ATOM 943 CD2 HIS B 66 38.083 1.535 6.904 1.00 71.25 C +ATOM 944 CE1 HIS B 66 40.044 1.135 7.804 1.00 73.08 C +ATOM 945 NE2 HIS B 66 39.319 0.967 6.711 1.00 73.26 N +ATOM 946 N ILE B 67 34.828 3.436 11.187 1.00 60.46 N +ATOM 947 CA ILE B 67 34.130 4.444 11.978 1.00 59.87 C +ATOM 948 C ILE B 67 34.229 4.139 13.471 1.00 59.99 C +ATOM 949 O ILE B 67 34.236 5.049 14.301 1.00 59.49 O +ATOM 950 CB ILE B 67 32.643 4.542 11.571 1.00 58.93 C +ATOM 951 CG1 ILE B 67 32.537 5.138 10.167 1.00 59.05 C +ATOM 952 CG2 ILE B 67 31.876 5.399 12.566 1.00 59.81 C +ATOM 953 CD1 ILE B 67 31.116 5.281 9.654 1.00 57.97 C +ATOM 954 N LEU B 68 34.310 2.860 13.814 1.00 60.11 N +ATOM 955 CA LEU B 68 34.407 2.491 15.212 1.00 63.74 C +ATOM 956 C LEU B 68 35.845 2.728 15.678 1.00 66.94 C +ATOM 957 O LEU B 68 36.604 1.791 15.919 1.00 66.18 O +ATOM 958 CB LEU B 68 33.973 1.031 15.402 1.00 62.06 C +ATOM 959 CG LEU B 68 32.573 0.710 14.844 1.00 61.98 C +ATOM 960 CD1 LEU B 68 32.119 -0.656 15.323 1.00 60.41 C +ATOM 961 CD2 LEU B 68 31.574 1.770 15.289 1.00 60.31 C +ATOM 962 N GLU B 69 36.193 4.010 15.785 1.00 71.13 N +ATOM 963 CA GLU B 69 37.523 4.465 16.196 1.00 74.13 C +ATOM 964 C GLU B 69 38.553 4.217 15.104 1.00 73.95 C +ATOM 965 O GLU B 69 39.205 3.153 15.138 1.00 74.87 O +ATOM 966 CB GLU B 69 37.958 3.785 17.498 1.00 76.89 C +ATOM 967 CG GLU B 69 37.002 4.039 18.650 1.00 80.52 C +ATOM 968 CD GLU B 69 36.708 5.517 18.848 1.00 82.53 C +ATOM 969 OE1 GLU B 69 37.373 6.154 19.693 1.00 84.32 O +ATOM 970 OE2 GLU B 69 35.819 6.044 18.143 1.00 83.58 O +TER 971 GLU B 69 diff --git a/example/protein-protein/1vf6_REC.pdb b/example/protein-protein/1vf6_REC.pdb new file mode 100644 index 0000000..f84cad9 --- /dev/null +++ b/example/protein-protein/1vf6_REC.pdb @@ -0,0 +1,477 @@ +ATOM 1 N VAL A 12 12.726 12.072 18.892 1.00 61.97 N +ATOM 2 CA VAL A 12 12.580 13.552 18.827 1.00 61.24 C +ATOM 3 C VAL A 12 13.162 14.210 20.069 1.00 61.44 C +ATOM 4 O VAL A 12 12.874 13.813 21.197 1.00 60.37 O +ATOM 5 CB VAL A 12 11.096 13.971 18.682 1.00 62.10 C +ATOM 6 CG1 VAL A 12 10.911 15.419 19.113 1.00 62.65 C +ATOM 7 CG2 VAL A 12 10.652 13.816 17.230 1.00 65.04 C +ATOM 8 N LEU A 13 13.989 15.223 19.844 1.00 61.43 N +ATOM 9 CA LEU A 13 14.623 15.951 20.925 1.00 60.82 C +ATOM 10 C LEU A 13 13.612 16.839 21.628 1.00 59.76 C +ATOM 11 O LEU A 13 13.781 17.163 22.798 1.00 60.40 O +ATOM 12 CB LEU A 13 15.775 16.792 20.376 1.00 61.26 C +ATOM 13 CG LEU A 13 16.884 15.969 19.718 1.00 62.73 C +ATOM 14 CD1 LEU A 13 17.846 16.892 18.992 1.00 64.99 C +ATOM 15 CD2 LEU A 13 17.616 15.149 20.775 1.00 63.07 C +ATOM 16 N GLN A 14 12.560 17.226 20.911 1.00 59.40 N +ATOM 17 CA GLN A 14 11.518 18.076 21.480 1.00 59.58 C +ATOM 18 C GLN A 14 10.752 17.308 22.556 1.00 56.77 C +ATOM 19 O GLN A 14 10.386 17.865 23.590 1.00 56.22 O +ATOM 20 CB GLN A 14 10.536 18.537 20.394 1.00 62.38 C +ATOM 21 CG GLN A 14 11.184 19.188 19.180 1.00 67.48 C +ATOM 22 CD GLN A 14 10.174 19.900 18.294 1.00 70.48 C +ATOM 23 OE1 GLN A 14 10.457 20.208 17.135 1.00 72.87 O +ATOM 24 NE2 GLN A 14 8.994 20.176 18.842 1.00 71.56 N +ATOM 25 N VAL A 15 10.506 16.029 22.295 1.00 55.31 N +ATOM 26 CA VAL A 15 9.797 15.175 23.241 1.00 53.16 C +ATOM 27 C VAL A 15 10.610 15.069 24.531 1.00 51.60 C +ATOM 28 O VAL A 15 10.100 15.334 25.617 1.00 49.70 O +ATOM 29 CB VAL A 15 9.573 13.763 22.646 1.00 54.11 C +ATOM 30 CG1 VAL A 15 9.045 12.818 23.716 1.00 53.75 C +ATOM 31 CG2 VAL A 15 8.584 13.843 21.485 1.00 54.91 C +ATOM 32 N LEU A 16 11.882 14.694 24.398 1.00 50.46 N +ATOM 33 CA LEU A 16 12.768 14.563 25.548 1.00 50.98 C +ATOM 34 C LEU A 16 12.795 15.846 26.348 1.00 50.30 C +ATOM 35 O LEU A 16 12.712 15.824 27.573 1.00 49.54 O +ATOM 36 CB LEU A 16 14.187 14.211 25.098 1.00 50.37 C +ATOM 37 CG LEU A 16 14.345 12.775 24.606 1.00 50.24 C +ATOM 38 CD1 LEU A 16 15.765 12.540 24.134 1.00 51.01 C +ATOM 39 CD2 LEU A 16 13.992 11.820 25.737 1.00 51.60 C +ATOM 40 N ASP A 17 12.911 16.967 25.645 1.00 51.75 N +ATOM 41 CA ASP A 17 12.939 18.267 26.290 1.00 52.78 C +ATOM 42 C ASP A 17 11.659 18.557 27.057 1.00 50.72 C +ATOM 43 O ASP A 17 11.708 19.016 28.190 1.00 50.88 O +ATOM 44 CB ASP A 17 13.188 19.358 25.248 1.00 57.28 C +ATOM 45 CG ASP A 17 14.664 19.669 25.075 1.00 61.34 C +ATOM 46 OD1 ASP A 17 15.032 20.222 24.016 1.00 64.58 O +ATOM 47 OD2 ASP A 17 15.454 19.370 26.002 1.00 63.15 O +ATOM 48 N ARG A 18 10.512 18.289 26.445 1.00 50.48 N +ATOM 49 CA ARG A 18 9.238 18.534 27.118 1.00 49.90 C +ATOM 50 C ARG A 18 9.075 17.644 28.351 1.00 48.87 C +ATOM 51 O ARG A 18 8.611 18.097 29.400 1.00 47.99 O +ATOM 52 CB ARG A 18 8.056 18.290 26.169 1.00 51.45 C +ATOM 53 CG ARG A 18 6.718 18.564 26.836 1.00 52.86 C +ATOM 54 CD ARG A 18 5.522 18.159 25.986 1.00 55.76 C +ATOM 55 NE ARG A 18 4.301 18.253 26.788 1.00 58.86 N +ATOM 56 CZ ARG A 18 3.992 17.423 27.784 1.00 59.17 C +ATOM 57 NH1 ARG A 18 4.808 16.424 28.094 1.00 59.35 N +ATOM 58 NH2 ARG A 18 2.885 17.612 28.494 1.00 57.80 N +ATOM 59 N LEU A 19 9.443 16.374 28.227 1.00 47.63 N +ATOM 60 CA LEU A 19 9.319 15.464 29.364 1.00 46.81 C +ATOM 61 C LEU A 19 10.185 15.931 30.531 1.00 47.18 C +ATOM 62 O LEU A 19 9.751 15.904 31.687 1.00 43.78 O +ATOM 63 CB LEU A 19 9.712 14.038 28.959 1.00 45.50 C +ATOM 64 CG LEU A 19 8.745 13.331 28.006 1.00 44.39 C +ATOM 65 CD1 LEU A 19 9.295 11.969 27.629 1.00 46.92 C +ATOM 66 CD2 LEU A 19 7.382 13.199 28.671 1.00 43.97 C +ATOM 67 N LYS A 20 11.408 16.366 30.238 1.00 49.36 N +ATOM 68 CA LYS A 20 12.298 16.826 31.308 1.00 53.34 C +ATOM 69 C LYS A 20 11.672 17.989 32.079 1.00 54.45 C +ATOM 70 O LYS A 20 11.730 18.036 33.310 1.00 55.35 O +ATOM 71 CB LYS A 20 13.666 17.241 30.745 1.00 54.49 C +ATOM 72 CG LYS A 20 14.700 17.519 31.840 1.00 59.05 C +ATOM 73 CD LYS A 20 16.137 17.402 31.340 1.00 61.92 C +ATOM 74 CE LYS A 20 16.459 18.435 30.269 1.00 65.59 C +ATOM 75 NZ LYS A 20 17.895 18.377 29.862 1.00 65.74 N +ATOM 76 N MET A 21 11.050 18.909 31.349 1.00 55.99 N +ATOM 77 CA MET A 21 10.405 20.065 31.955 1.00 57.04 C +ATOM 78 C MET A 21 9.176 19.682 32.788 1.00 56.20 C +ATOM 79 O MET A 21 8.968 20.216 33.877 1.00 55.42 O +ATOM 80 CB MET A 21 10.019 21.065 30.860 1.00 61.44 C +ATOM 81 CG MET A 21 9.283 22.303 31.354 1.00 68.45 C +ATOM 82 SD MET A 21 9.254 23.620 30.102 1.00 79.55 S +ATOM 83 CE MET A 21 7.920 23.063 29.003 1.00 76.73 C +ATOM 84 N LYS A 22 8.358 18.763 32.282 1.00 54.57 N +ATOM 85 CA LYS A 22 7.166 18.340 33.014 1.00 53.51 C +ATOM 86 C LYS A 22 7.540 17.638 34.314 1.00 52.42 C +ATOM 87 O LYS A 22 6.802 17.705 35.297 1.00 52.51 O +ATOM 88 CB LYS A 22 6.313 17.407 32.155 1.00 54.44 C +ATOM 89 CG LYS A 22 5.709 18.081 30.935 1.00 57.81 C +ATOM 90 CD LYS A 22 4.223 18.342 31.112 1.00 60.53 C +ATOM 91 CE LYS A 22 3.926 19.276 32.270 1.00 62.83 C +ATOM 92 NZ LYS A 22 2.453 19.407 32.486 1.00 63.90 N +ATOM 93 N LEU A 23 8.679 16.953 34.313 1.00 51.71 N +ATOM 94 CA LEU A 23 9.139 16.257 35.510 1.00 52.44 C +ATOM 95 C LEU A 23 9.602 17.284 36.534 1.00 54.43 C +ATOM 96 O LEU A 23 9.314 17.152 37.729 1.00 53.59 O +ATOM 97 CB LEU A 23 10.283 15.298 35.168 1.00 49.24 C +ATOM 98 CG LEU A 23 9.855 14.067 34.361 1.00 48.95 C +ATOM 99 CD1 LEU A 23 11.076 13.327 33.837 1.00 47.45 C +ATOM 100 CD2 LEU A 23 8.996 13.161 35.238 1.00 46.50 C +ATOM 101 N GLN A 24 10.314 18.306 36.055 1.00 56.26 N +ATOM 102 CA GLN A 24 10.808 19.380 36.915 1.00 58.68 C +ATOM 103 C GLN A 24 9.607 19.984 37.634 1.00 59.03 C +ATOM 104 O GLN A 24 9.609 20.162 38.850 1.00 58.60 O +ATOM 105 CB GLN A 24 11.462 20.490 36.085 1.00 61.44 C +ATOM 106 CG GLN A 24 12.512 20.049 35.080 1.00 65.59 C +ATOM 107 CD GLN A 24 13.825 19.674 35.720 1.00 67.88 C +ATOM 108 OE1 GLN A 24 14.812 19.406 35.029 1.00 68.94 O +ATOM 109 NE2 GLN A 24 13.851 19.651 37.050 1.00 71.36 N +ATOM 110 N GLU A 25 8.582 20.298 36.853 1.00 60.21 N +ATOM 111 CA GLU A 25 7.367 20.898 37.371 1.00 62.31 C +ATOM 112 C GLU A 25 6.727 20.071 38.476 1.00 62.06 C +ATOM 113 O GLU A 25 6.145 20.626 39.407 1.00 61.65 O +ATOM 114 CB GLU A 25 6.366 21.105 36.236 1.00 65.10 C +ATOM 115 CG GLU A 25 6.845 22.048 35.148 1.00 68.59 C +ATOM 116 CD GLU A 25 5.841 22.163 34.017 1.00 73.11 C +ATOM 117 OE1 GLU A 25 6.135 22.860 33.020 1.00 74.20 O +ATOM 118 OE2 GLU A 25 4.752 21.551 34.130 1.00 75.33 O +ATOM 119 N LYS A 26 6.821 18.748 38.368 1.00 60.86 N +ATOM 120 CA LYS A 26 6.240 17.871 39.383 1.00 61.60 C +ATOM 121 C LYS A 26 7.147 17.714 40.589 1.00 59.82 C +ATOM 122 O LYS A 26 6.735 17.179 41.615 1.00 60.83 O +ATOM 123 CB LYS A 26 5.940 16.484 38.810 1.00 62.57 C +ATOM 124 CG LYS A 26 4.584 16.361 38.152 1.00 65.15 C +ATOM 125 CD LYS A 26 4.055 14.944 38.311 1.00 68.18 C +ATOM 126 CE LYS A 26 2.607 14.839 37.866 1.00 70.27 C +ATOM 127 NZ LYS A 26 2.015 13.524 38.227 1.00 72.00 N +ATOM 128 N GLY A 27 8.383 18.180 40.461 1.00 58.97 N +ATOM 129 CA GLY A 27 9.327 18.067 41.555 1.00 58.20 C +ATOM 130 C GLY A 27 10.110 16.770 41.485 1.00 57.33 C +ATOM 131 O GLY A 27 10.728 16.361 42.468 1.00 56.87 O +ATOM 132 N ASP A 28 10.083 16.122 40.322 1.00 55.08 N +ATOM 133 CA ASP A 28 10.796 14.864 40.118 1.00 53.68 C +ATOM 134 C ASP A 28 12.001 15.105 39.220 1.00 53.07 C +ATOM 135 O ASP A 28 11.846 15.311 38.017 1.00 53.33 O +ATOM 136 CB ASP A 28 9.870 13.828 39.469 1.00 51.00 C +ATOM 137 CG ASP A 28 10.545 12.476 39.272 1.00 52.44 C +ATOM 138 OD1 ASP A 28 9.890 11.556 38.741 1.00 51.58 O +ATOM 139 OD2 ASP A 28 11.729 12.328 39.643 1.00 50.22 O +ATOM 140 N THR A 29 13.198 15.090 39.806 1.00 53.45 N +ATOM 141 CA THR A 29 14.427 15.313 39.045 1.00 53.56 C +ATOM 142 C THR A 29 15.269 14.051 38.965 1.00 51.72 C +ATOM 143 O THR A 29 16.451 14.097 38.630 1.00 53.05 O +ATOM 144 CB THR A 29 15.291 16.440 39.658 1.00 55.63 C +ATOM 145 OG1 THR A 29 15.483 16.195 41.058 1.00 57.59 O +ATOM 146 CG2 THR A 29 14.626 17.791 39.455 1.00 57.62 C +ATOM 147 N SER A 30 14.650 12.920 39.267 1.00 50.50 N +ATOM 148 CA SER A 30 15.344 11.641 39.222 1.00 50.77 C +ATOM 149 C SER A 30 15.841 11.262 37.819 1.00 49.99 C +ATOM 150 O SER A 30 16.733 10.428 37.678 1.00 49.10 O +ATOM 151 CB SER A 30 14.419 10.540 39.737 1.00 50.39 C +ATOM 152 OG SER A 30 13.270 10.416 38.910 1.00 51.14 O +ATOM 153 N GLN A 31 15.266 11.869 36.787 1.00 50.92 N +ATOM 154 CA GLN A 31 15.649 11.538 35.418 1.00 52.52 C +ATOM 155 C GLN A 31 16.357 12.653 34.649 1.00 54.61 C +ATOM 156 O GLN A 31 16.613 12.508 33.456 1.00 54.57 O +ATOM 157 CB GLN A 31 14.415 11.094 34.626 1.00 50.57 C +ATOM 158 CG GLN A 31 13.604 9.980 35.272 1.00 49.91 C +ATOM 159 CD GLN A 31 14.451 8.782 35.666 1.00 50.22 C +ATOM 160 OE1 GLN A 31 15.276 8.303 34.889 1.00 52.22 O +ATOM 161 NE2 GLN A 31 14.244 8.289 36.879 1.00 50.51 N +ATOM 162 N ASN A 32 16.676 13.759 35.317 1.00 56.46 N +ATOM 163 CA ASN A 32 17.358 14.866 34.648 1.00 58.80 C +ATOM 164 C ASN A 32 18.577 14.400 33.861 1.00 58.43 C +ATOM 165 O ASN A 32 18.673 14.634 32.658 1.00 58.69 O +ATOM 166 CB ASN A 32 17.811 15.919 35.662 1.00 63.62 C +ATOM 167 CG ASN A 32 16.687 16.841 36.094 1.00 68.12 C +ATOM 168 OD1 ASN A 32 16.870 17.704 36.959 1.00 71.44 O +ATOM 169 ND2 ASN A 32 15.522 16.672 35.492 1.00 69.00 N +ATOM 170 N GLU A 33 19.502 13.741 34.551 1.00 58.50 N +ATOM 171 CA GLU A 33 20.740 13.257 33.948 1.00 59.57 C +ATOM 172 C GLU A 33 20.536 12.175 32.892 1.00 58.08 C +ATOM 173 O GLU A 33 21.156 12.211 31.827 1.00 57.90 O +ATOM 174 CB GLU A 33 21.672 12.722 35.039 1.00 62.86 C +ATOM 175 CG GLU A 33 23.053 12.326 34.536 1.00 70.35 C +ATOM 176 CD GLU A 33 23.841 11.522 35.555 1.00 74.10 C +ATOM 177 OE1 GLU A 33 23.391 10.407 35.915 1.00 76.08 O +ATOM 178 OE2 GLU A 33 24.908 12.007 35.997 1.00 76.68 O +ATOM 179 N LYS A 34 19.678 11.207 33.199 1.00 56.20 N +ATOM 180 CA LYS A 34 19.400 10.109 32.279 1.00 53.83 C +ATOM 181 C LYS A 34 18.908 10.650 30.936 1.00 50.58 C +ATOM 182 O LYS A 34 19.413 10.272 29.880 1.00 49.42 O +ATOM 183 CB LYS A 34 18.339 9.181 32.874 1.00 57.27 C +ATOM 184 CG LYS A 34 18.306 7.785 32.261 1.00 61.67 C +ATOM 185 CD LYS A 34 19.247 6.832 32.997 1.00 65.89 C +ATOM 186 CE LYS A 34 18.845 6.694 34.472 1.00 68.32 C +ATOM 187 NZ LYS A 34 19.617 5.639 35.200 1.00 69.21 N +ATOM 188 N LEU A 35 17.919 11.535 30.986 1.00 45.98 N +ATOM 189 CA LEU A 35 17.363 12.124 29.778 1.00 46.72 C +ATOM 190 C LEU A 35 18.397 12.945 28.999 1.00 46.77 C +ATOM 191 O LEU A 35 18.471 12.860 27.773 1.00 44.75 O +ATOM 192 CB LEU A 35 16.155 12.996 30.128 1.00 44.93 C +ATOM 193 CG LEU A 35 14.907 12.239 30.589 1.00 45.62 C +ATOM 194 CD1 LEU A 35 13.867 13.224 31.094 1.00 44.92 C +ATOM 195 CD2 LEU A 35 14.359 11.411 29.439 1.00 43.93 C +ATOM 196 N SER A 36 19.195 13.738 29.706 1.00 46.75 N +ATOM 197 CA SER A 36 20.211 14.540 29.038 1.00 48.05 C +ATOM 198 C SER A 36 21.219 13.640 28.327 1.00 47.46 C +ATOM 199 O SER A 36 21.620 13.927 27.204 1.00 48.97 O +ATOM 200 CB SER A 36 20.920 15.454 30.044 1.00 48.89 C +ATOM 201 OG SER A 36 20.005 16.416 30.555 1.00 50.93 O +ATOM 202 N MET A 37 21.615 12.547 28.972 1.00 48.57 N +ATOM 203 CA MET A 37 22.561 11.616 28.364 1.00 50.66 C +ATOM 204 C MET A 37 21.920 10.959 27.141 1.00 49.23 C +ATOM 205 O MET A 37 22.557 10.795 26.099 1.00 47.90 O +ATOM 206 CB MET A 37 22.980 10.536 29.368 1.00 56.24 C +ATOM 207 CG MET A 37 23.729 11.070 30.590 1.00 64.70 C +ATOM 208 SD MET A 37 24.491 9.757 31.592 1.00 74.41 S +ATOM 209 CE MET A 37 23.168 9.418 32.799 1.00 71.50 C +ATOM 210 N PHE A 38 20.658 10.569 27.279 1.00 47.12 N +ATOM 211 CA PHE A 38 19.945 9.954 26.174 1.00 44.02 C +ATOM 212 C PHE A 38 19.957 10.980 25.047 1.00 42.93 C +ATOM 213 O PHE A 38 20.298 10.676 23.899 1.00 41.03 O +ATOM 214 CB PHE A 38 18.510 9.630 26.608 1.00 46.73 C +ATOM 215 CG PHE A 38 17.696 8.908 25.565 1.00 47.72 C +ATOM 216 CD1 PHE A 38 18.289 7.994 24.700 1.00 48.65 C +ATOM 217 CD2 PHE A 38 16.323 9.117 25.476 1.00 50.44 C +ATOM 218 CE1 PHE A 38 17.523 7.297 23.758 1.00 50.56 C +ATOM 219 CE2 PHE A 38 15.549 8.424 24.536 1.00 50.20 C +ATOM 220 CZ PHE A 38 16.153 7.516 23.679 1.00 49.12 C +ATOM 221 N TYR A 39 19.604 12.209 25.405 1.00 42.33 N +ATOM 222 CA TYR A 39 19.551 13.319 24.470 1.00 44.40 C +ATOM 223 C TYR A 39 20.875 13.495 23.715 1.00 45.65 C +ATOM 224 O TYR A 39 20.888 13.598 22.486 1.00 42.26 O +ATOM 225 CB TYR A 39 19.232 14.596 25.246 1.00 50.50 C +ATOM 226 CG TYR A 39 19.000 15.823 24.404 1.00 55.27 C +ATOM 227 CD1 TYR A 39 17.706 16.259 24.122 1.00 58.05 C +ATOM 228 CD2 TYR A 39 20.070 16.559 23.899 1.00 57.16 C +ATOM 229 CE1 TYR A 39 17.481 17.401 23.361 1.00 61.04 C +ATOM 230 CE2 TYR A 39 19.860 17.703 23.131 1.00 59.43 C +ATOM 231 CZ TYR A 39 18.562 18.119 22.866 1.00 61.29 C +ATOM 232 OH TYR A 39 18.340 19.248 22.106 1.00 64.11 O +ATOM 233 N GLU A 40 21.984 13.524 24.456 1.00 45.02 N +ATOM 234 CA GLU A 40 23.302 13.713 23.851 1.00 45.29 C +ATOM 235 C GLU A 40 23.694 12.559 22.949 1.00 44.03 C +ATOM 236 O GLU A 40 24.372 12.747 21.941 1.00 42.26 O +ATOM 237 CB GLU A 40 24.363 13.911 24.941 1.00 49.34 C +ATOM 238 CG GLU A 40 24.197 15.218 25.711 1.00 54.69 C +ATOM 239 CD GLU A 40 24.253 16.439 24.807 1.00 59.26 C +ATOM 240 OE1 GLU A 40 23.695 17.490 25.192 1.00 61.80 O +ATOM 241 OE2 GLU A 40 24.859 16.353 23.712 1.00 62.65 O +ATOM 242 N THR A 41 23.272 11.354 23.308 1.00 43.92 N +ATOM 243 CA THR A 41 23.587 10.201 22.481 1.00 43.24 C +ATOM 244 C THR A 41 22.890 10.295 21.125 1.00 41.62 C +ATOM 245 O THR A 41 23.504 10.072 20.086 1.00 41.17 O +ATOM 246 CB THR A 41 23.168 8.902 23.166 1.00 43.87 C +ATOM 247 OG1 THR A 41 23.885 8.772 24.398 1.00 45.63 O +ATOM 248 CG2 THR A 41 23.480 7.704 22.271 1.00 44.45 C +ATOM 249 N LEU A 42 21.609 10.641 21.139 1.00 43.09 N +ATOM 250 CA LEU A 42 20.834 10.751 19.906 1.00 44.18 C +ATOM 251 C LEU A 42 21.370 11.852 18.999 1.00 45.02 C +ATOM 252 O LEU A 42 21.257 11.773 17.783 1.00 44.53 O +ATOM 253 CB LEU A 42 19.360 11.025 20.237 1.00 44.21 C +ATOM 254 CG LEU A 42 18.635 9.937 21.044 1.00 45.38 C +ATOM 255 CD1 LEU A 42 17.297 10.457 21.541 1.00 45.14 C +ATOM 256 CD2 LEU A 42 18.446 8.697 20.177 1.00 45.21 C +ATOM 257 N LYS A 43 21.970 12.870 19.600 1.00 45.36 N +ATOM 258 CA LYS A 43 22.514 14.005 18.861 1.00 47.05 C +ATOM 259 C LYS A 43 23.974 13.750 18.474 1.00 47.43 C +ATOM 260 O LYS A 43 24.546 14.461 17.652 1.00 47.49 O +ATOM 261 CB LYS A 43 22.422 15.252 19.747 1.00 49.70 C +ATOM 262 CG LYS A 43 21.973 16.526 19.054 1.00 54.27 C +ATOM 263 CD LYS A 43 21.815 17.647 20.073 1.00 57.18 C +ATOM 264 CE LYS A 43 23.101 17.845 20.889 1.00 59.95 C +ATOM 265 NZ LYS A 43 22.953 18.868 21.967 1.00 60.80 N +ATOM 266 N SER A 44 24.561 12.723 19.075 1.00 46.17 N +ATOM 267 CA SER A 44 25.951 12.357 18.852 1.00 45.94 C +ATOM 268 C SER A 44 26.363 12.046 17.409 1.00 46.08 C +ATOM 269 O SER A 44 25.699 11.286 16.704 1.00 43.09 O +ATOM 270 CB SER A 44 26.292 11.164 19.748 1.00 45.91 C +ATOM 271 OG SER A 44 27.479 10.526 19.321 1.00 51.21 O +ATOM 272 N PRO A 45 27.477 12.644 16.946 1.00 46.13 N +ATOM 273 CA PRO A 45 27.916 12.369 15.577 1.00 45.08 C +ATOM 274 C PRO A 45 28.193 10.891 15.353 1.00 44.02 C +ATOM 275 O PRO A 45 27.758 10.322 14.362 1.00 43.57 O +ATOM 276 CB PRO A 45 29.162 13.251 15.414 1.00 46.80 C +ATOM 277 CG PRO A 45 29.534 13.654 16.803 1.00 48.64 C +ATOM 278 CD PRO A 45 28.225 13.777 17.514 1.00 47.38 C +ATOM 279 N LEU A 46 28.903 10.260 16.281 1.00 42.61 N +ATOM 280 CA LEU A 46 29.196 8.842 16.152 1.00 41.71 C +ATOM 281 C LEU A 46 27.917 8.001 16.036 1.00 41.39 C +ATOM 282 O LEU A 46 27.834 7.108 15.196 1.00 40.12 O +ATOM 283 CB LEU A 46 30.008 8.349 17.353 1.00 43.77 C +ATOM 284 CG LEU A 46 30.245 6.838 17.421 1.00 44.72 C +ATOM 285 CD1 LEU A 46 30.946 6.367 16.156 1.00 46.37 C +ATOM 286 CD2 LEU A 46 31.071 6.503 18.645 1.00 48.99 C +ATOM 287 N PHE A 47 26.935 8.287 16.890 1.00 40.31 N +ATOM 288 CA PHE A 47 25.668 7.552 16.900 1.00 40.01 C +ATOM 289 C PHE A 47 24.941 7.692 15.571 1.00 39.19 C +ATOM 290 O PHE A 47 24.392 6.723 15.048 1.00 39.05 O +ATOM 291 CB PHE A 47 24.754 8.069 18.015 1.00 41.79 C +ATOM 292 CG PHE A 47 23.470 7.302 18.150 1.00 43.26 C +ATOM 293 CD1 PHE A 47 23.469 6.010 18.674 1.00 43.17 C +ATOM 294 CD2 PHE A 47 22.260 7.870 17.755 1.00 44.02 C +ATOM 295 CE1 PHE A 47 22.283 5.295 18.808 1.00 44.89 C +ATOM 296 CE2 PHE A 47 21.062 7.160 17.885 1.00 47.15 C +ATOM 297 CZ PHE A 47 21.074 5.870 18.414 1.00 44.20 C +ATOM 298 N ASN A 48 24.947 8.907 15.034 1.00 37.22 N +ATOM 299 CA ASN A 48 24.286 9.181 13.772 1.00 38.92 C +ATOM 300 C ASN A 48 24.976 8.513 12.594 1.00 40.33 C +ATOM 301 O ASN A 48 24.308 8.068 11.648 1.00 38.77 O +ATOM 302 CB ASN A 48 24.159 10.690 13.585 1.00 38.44 C +ATOM 303 CG ASN A 48 22.990 11.257 14.369 1.00 41.34 C +ATOM 304 OD1 ASN A 48 21.870 11.318 13.864 1.00 43.63 O +ATOM 305 ND2 ASN A 48 23.234 11.640 15.616 1.00 40.66 N +ATOM 306 N GLN A 49 26.303 8.419 12.653 1.00 36.17 N +ATOM 307 CA GLN A 49 27.049 7.750 11.597 1.00 37.58 C +ATOM 308 C GLN A 49 26.737 6.249 11.642 1.00 37.39 C +ATOM 309 O GLN A 49 26.544 5.619 10.601 1.00 35.87 O +ATOM 310 CB GLN A 49 28.563 7.960 11.777 1.00 38.98 C +ATOM 311 CG GLN A 49 29.046 9.380 11.465 1.00 40.40 C +ATOM 312 CD GLN A 49 30.533 9.562 11.735 1.00 47.22 C +ATOM 313 OE1 GLN A 49 31.310 8.598 11.692 1.00 44.32 O +ATOM 314 NE2 GLN A 49 30.939 10.805 12.006 1.00 46.26 N +ATOM 315 N ILE A 50 26.692 5.683 12.849 1.00 37.01 N +ATOM 316 CA ILE A 50 26.411 4.254 13.023 1.00 37.62 C +ATOM 317 C ILE A 50 24.991 3.897 12.559 1.00 38.24 C +ATOM 318 O ILE A 50 24.808 2.912 11.848 1.00 39.72 O +ATOM 319 CB ILE A 50 26.586 3.819 14.495 1.00 38.38 C +ATOM 320 CG1 ILE A 50 28.036 4.028 14.932 1.00 40.19 C +ATOM 321 CG2 ILE A 50 26.191 2.347 14.658 1.00 37.94 C +ATOM 322 CD1 ILE A 50 28.281 3.750 16.410 1.00 43.17 C +ATOM 323 N LEU A 51 24.003 4.700 12.954 1.00 37.27 N +ATOM 324 CA LEU A 51 22.612 4.475 12.548 1.00 40.22 C +ATOM 325 C LEU A 51 22.486 4.456 11.033 1.00 38.66 C +ATOM 326 O LEU A 51 21.912 3.527 10.455 1.00 38.65 O +ATOM 327 CB LEU A 51 21.686 5.587 13.070 1.00 40.44 C +ATOM 328 CG LEU A 51 20.923 5.445 14.387 1.00 45.08 C +ATOM 329 CD1 LEU A 51 19.974 6.634 14.527 1.00 44.87 C +ATOM 330 CD2 LEU A 51 20.131 4.144 14.407 1.00 43.80 C +ATOM 331 N THR A 52 23.010 5.508 10.405 1.00 37.04 N +ATOM 332 CA THR A 52 22.963 5.669 8.965 1.00 35.67 C +ATOM 333 C THR A 52 23.585 4.474 8.249 1.00 38.21 C +ATOM 334 O THR A 52 22.987 3.915 7.321 1.00 37.77 O +ATOM 335 CB THR A 52 23.694 6.959 8.536 1.00 36.10 C +ATOM 336 OG1 THR A 52 23.113 8.075 9.210 1.00 37.70 O +ATOM 337 CG2 THR A 52 23.573 7.189 7.035 1.00 35.47 C +ATOM 338 N LEU A 53 24.778 4.077 8.685 1.00 37.57 N +ATOM 339 CA LEU A 53 25.473 2.953 8.060 1.00 38.41 C +ATOM 340 C LEU A 53 24.775 1.610 8.249 1.00 36.51 C +ATOM 341 O LEU A 53 24.745 0.785 7.337 1.00 35.49 O +ATOM 342 CB LEU A 53 26.907 2.854 8.584 1.00 38.51 C +ATOM 343 CG LEU A 53 27.975 2.928 7.487 1.00 44.14 C +ATOM 344 CD1 LEU A 53 29.359 2.924 8.132 1.00 46.06 C +ATOM 345 CD2 LEU A 53 27.820 1.756 6.512 1.00 40.49 C +ATOM 346 N GLN A 54 24.242 1.373 9.440 1.00 37.65 N +ATOM 347 CA GLN A 54 23.541 0.122 9.688 1.00 40.23 C +ATOM 348 C GLN A 54 22.273 0.005 8.827 1.00 37.93 C +ATOM 349 O GLN A 54 21.931 -1.089 8.375 1.00 38.52 O +ATOM 350 CB GLN A 54 23.238 -0.012 11.177 1.00 43.22 C +ATOM 351 CG GLN A 54 24.469 -0.518 11.939 1.00 49.98 C +ATOM 352 CD GLN A 54 24.267 -0.622 13.438 1.00 54.12 C +ATOM 353 OE1 GLN A 54 24.925 -1.424 14.105 1.00 57.10 O +ATOM 354 NE2 GLN A 54 23.372 0.195 13.979 1.00 54.06 N +ATOM 355 N GLN A 55 21.611 1.132 8.570 1.00 37.04 N +ATOM 356 CA GLN A 55 20.414 1.138 7.732 1.00 38.60 C +ATOM 357 C GLN A 55 20.833 0.800 6.304 1.00 37.87 C +ATOM 358 O GLN A 55 20.107 0.124 5.581 1.00 34.11 O +ATOM 359 CB GLN A 55 19.719 2.510 7.746 1.00 37.06 C +ATOM 360 CG GLN A 55 18.826 2.749 8.963 1.00 46.62 C +ATOM 361 CD GLN A 55 17.750 1.672 9.115 1.00 50.03 C +ATOM 362 OE1 GLN A 55 17.033 1.351 8.157 1.00 50.51 O +ATOM 363 NE2 GLN A 55 17.636 1.113 10.314 1.00 46.65 N +ATOM 364 N SER A 56 22.001 1.286 5.894 1.00 36.63 N +ATOM 365 CA SER A 56 22.500 0.990 4.545 1.00 36.24 C +ATOM 366 C SER A 56 22.813 -0.503 4.418 1.00 34.94 C +ATOM 367 O SER A 56 22.473 -1.132 3.428 1.00 35.77 O +ATOM 368 CB SER A 56 23.758 1.809 4.243 1.00 37.34 C +ATOM 369 OG SER A 56 23.460 3.193 4.211 1.00 35.52 O +ATOM 370 N ILE A 57 23.455 -1.071 5.427 1.00 35.54 N +ATOM 371 CA ILE A 57 23.785 -2.491 5.389 1.00 37.18 C +ATOM 372 C ILE A 57 22.481 -3.298 5.433 1.00 38.87 C +ATOM 373 O ILE A 57 22.348 -4.325 4.766 1.00 36.62 O +ATOM 374 CB ILE A 57 24.706 -2.865 6.575 1.00 37.59 C +ATOM 375 CG1 ILE A 57 26.064 -2.172 6.400 1.00 37.72 C +ATOM 376 CG2 ILE A 57 24.862 -4.365 6.668 1.00 37.97 C +ATOM 377 CD1 ILE A 57 27.006 -2.355 7.582 1.00 36.89 C +ATOM 378 N LYS A 58 21.514 -2.809 6.206 1.00 39.48 N +ATOM 379 CA LYS A 58 20.214 -3.462 6.308 1.00 40.43 C +ATOM 380 C LYS A 58 19.543 -3.512 4.933 1.00 38.91 C +ATOM 381 O LYS A 58 18.972 -4.533 4.552 1.00 38.87 O +ATOM 382 CB LYS A 58 19.318 -2.704 7.298 1.00 44.69 C +ATOM 383 CG LYS A 58 18.018 -3.414 7.622 1.00 49.92 C +ATOM 384 CD LYS A 58 17.149 -2.598 8.580 1.00 53.81 C +ATOM 385 CE LYS A 58 15.903 -3.377 8.988 1.00 56.71 C +ATOM 386 NZ LYS A 58 14.903 -2.524 9.694 1.00 60.38 N +ATOM 387 N GLN A 59 19.617 -2.416 4.182 1.00 35.98 N +ATOM 388 CA GLN A 59 19.012 -2.374 2.855 1.00 39.08 C +ATOM 389 C GLN A 59 19.683 -3.354 1.874 1.00 41.36 C +ATOM 390 O GLN A 59 18.999 -3.980 1.056 1.00 37.25 O +ATOM 391 CB GLN A 59 19.060 -0.947 2.288 1.00 44.00 C +ATOM 392 CG GLN A 59 18.133 0.037 3.012 1.00 51.28 C +ATOM 393 CD GLN A 59 18.329 1.498 2.590 1.00 57.43 C +ATOM 394 OE1 GLN A 59 17.586 2.382 3.038 1.00 60.68 O +ATOM 395 NE2 GLN A 59 19.336 1.761 1.741 1.00 56.30 N +ATOM 396 N LEU A 60 21.014 -3.481 1.951 1.00 37.18 N +ATOM 397 CA LEU A 60 21.743 -4.402 1.074 1.00 38.83 C +ATOM 398 C LEU A 60 21.328 -5.842 1.379 1.00 37.25 C +ATOM 399 O LEU A 60 21.171 -6.655 0.467 1.00 36.67 O +ATOM 400 CB LEU A 60 23.269 -4.268 1.262 1.00 36.23 C +ATOM 401 CG LEU A 60 23.939 -2.966 0.825 1.00 37.53 C +ATOM 402 CD1 LEU A 60 25.468 -3.060 1.069 1.00 39.65 C +ATOM 403 CD2 LEU A 60 23.654 -2.708 -0.635 1.00 34.28 C +ATOM 404 N LYS A 61 21.167 -6.152 2.664 1.00 39.24 N +ATOM 405 CA LYS A 61 20.761 -7.497 3.078 1.00 43.00 C +ATOM 406 C LYS A 61 19.341 -7.799 2.603 1.00 44.27 C +ATOM 407 O LYS A 61 19.015 -8.943 2.282 1.00 46.34 O +ATOM 408 CB LYS A 61 20.832 -7.639 4.597 1.00 44.53 C +ATOM 409 CG LYS A 61 22.244 -7.732 5.146 1.00 47.15 C +ATOM 410 CD LYS A 61 22.224 -7.869 6.653 1.00 49.30 C +ATOM 411 CE LYS A 61 23.622 -8.030 7.212 1.00 51.89 C +ATOM 412 NZ LYS A 61 23.601 -8.233 8.694 1.00 56.40 N +ATOM 413 N GLY A 62 18.506 -6.765 2.555 1.00 44.54 N +ATOM 414 CA GLY A 62 17.140 -6.927 2.096 1.00 43.11 C +ATOM 415 C GLY A 62 17.157 -7.152 0.599 1.00 43.50 C +ATOM 416 O GLY A 62 16.343 -7.898 0.060 1.00 41.08 O +ATOM 417 N GLN A 63 18.088 -6.493 -0.083 1.00 43.85 N +ATOM 418 CA GLN A 63 18.216 -6.660 -1.524 1.00 45.04 C +ATOM 419 C GLN A 63 18.633 -8.108 -1.795 1.00 46.42 C +ATOM 420 O GLN A 63 18.155 -8.740 -2.740 1.00 46.52 O +ATOM 421 CB GLN A 63 19.260 -5.693 -2.080 1.00 42.40 C +ATOM 422 CG GLN A 63 19.478 -5.793 -3.582 1.00 40.05 C +ATOM 423 CD GLN A 63 20.572 -4.854 -4.080 1.00 37.58 C +ATOM 424 OE1 GLN A 63 20.905 -4.842 -5.265 1.00 39.63 O +ATOM 425 NE2 GLN A 63 21.129 -4.060 -3.174 1.00 32.22 N +ATOM 426 N LEU A 64 19.509 -8.636 -0.946 1.00 48.69 N +ATOM 427 CA LEU A 64 19.979 -10.013 -1.085 1.00 50.70 C +ATOM 428 C LEU A 64 18.790 -10.957 -0.917 1.00 52.75 C +ATOM 429 O LEU A 64 18.481 -11.740 -1.811 1.00 51.58 O +ATOM 430 CB LEU A 64 21.023 -10.335 -0.019 1.00 50.20 C +ATOM 431 CG LEU A 64 22.185 -11.272 -0.376 1.00 53.81 C +ATOM 432 CD1 LEU A 64 22.739 -11.850 0.915 1.00 52.27 C +ATOM 433 CD2 LEU A 64 21.744 -12.394 -1.318 1.00 51.50 C +ATOM 434 N ASN A 65 18.128 -10.875 0.237 1.00 56.37 N +ATOM 435 CA ASN A 65 16.961 -11.712 0.526 1.00 58.61 C +ATOM 436 C ASN A 65 15.971 -11.704 -0.627 1.00 58.46 C +ATOM 437 O ASN A 65 15.379 -12.730 -0.960 1.00 58.19 O +ATOM 438 CB ASN A 65 16.263 -11.230 1.800 1.00 61.07 C +ATOM 439 CG ASN A 65 17.093 -11.468 3.037 1.00 63.88 C +ATOM 440 OD1 ASN A 65 16.723 -11.054 4.136 1.00 68.06 O +ATOM 441 ND2 ASN A 65 18.227 -12.143 2.870 1.00 65.98 N +ATOM 442 N HIS A 66 15.788 -10.542 -1.234 1.00 59.03 N +ATOM 443 CA HIS A 66 14.878 -10.432 -2.355 1.00 62.20 C +ATOM 444 C HIS A 66 15.414 -11.317 -3.479 1.00 64.60 C +ATOM 445 O HIS A 66 14.739 -12.244 -3.929 1.00 66.44 O +ATOM 446 CB HIS A 66 14.797 -8.983 -2.825 1.00 65.23 C +ATOM 447 CG HIS A 66 13.565 -8.674 -3.613 1.00 68.80 C +ATOM 448 ND1 HIS A 66 12.306 -8.669 -3.051 1.00 69.91 N +ATOM 449 CD2 HIS A 66 13.395 -8.372 -4.922 1.00 70.18 C +ATOM 450 CE1 HIS A 66 11.413 -8.376 -3.980 1.00 71.22 C +ATOM 451 NE2 HIS A 66 12.048 -8.190 -5.124 1.00 72.24 N +ATOM 452 N ILE A 67 16.639 -11.032 -3.918 1.00 64.91 N +ATOM 453 CA ILE A 67 17.285 -11.794 -4.982 1.00 64.46 C +ATOM 454 C ILE A 67 17.056 -13.289 -4.825 1.00 64.87 C +ATOM 455 O ILE A 67 16.764 -13.982 -5.795 1.00 65.64 O +ATOM 456 CB ILE A 67 18.803 -11.509 -5.019 1.00 63.69 C +ATOM 457 CG1 ILE A 67 19.050 -10.185 -5.741 1.00 63.90 C +ATOM 458 CG2 ILE A 67 19.552 -12.654 -5.691 1.00 63.42 C +ATOM 459 CD1 ILE A 67 20.498 -9.769 -5.783 1.00 64.63 C +ATOM 460 N LEU A 68 17.195 -13.785 -3.603 1.00 66.19 N +ATOM 461 CA LEU A 68 16.988 -15.199 -3.335 1.00 68.55 C +ATOM 462 C LEU A 68 15.495 -15.532 -3.419 1.00 72.23 C +ATOM 463 O LEU A 68 14.811 -15.664 -2.402 1.00 73.14 O +ATOM 464 CB LEU A 68 17.554 -15.549 -1.958 1.00 65.44 C +ATOM 465 CG LEU A 68 19.060 -15.280 -1.847 1.00 64.10 C +ATOM 466 CD1 LEU A 68 19.529 -15.474 -0.423 1.00 62.60 C +ATOM 467 CD2 LEU A 68 19.817 -16.205 -2.787 1.00 63.73 C +ATOM 468 N GLU A 69 15.011 -15.652 -4.655 1.00 75.96 N +ATOM 469 CA GLU A 69 13.614 -15.961 -4.968 1.00 78.80 C +ATOM 470 C GLU A 69 12.627 -14.949 -4.397 1.00 79.79 C +ATOM 471 O GLU A 69 11.942 -14.287 -5.208 1.00 80.93 O +ATOM 472 CB GLU A 69 13.247 -17.367 -4.476 1.00 80.58 C +ATOM 473 CG GLU A 69 14.211 -18.473 -4.912 1.00 83.04 C +ATOM 474 CD GLU A 69 14.881 -18.189 -6.248 1.00 84.52 C +ATOM 475 OE1 GLU A 69 14.169 -17.852 -7.219 1.00 84.91 O +ATOM 476 OE2 GLU A 69 16.125 -18.307 -6.326 1.00 85.17 O +TER 477 GLU A 69 diff --git a/example/protein-protein/default.ini b/example/protein-protein/default.ini new file mode 100644 index 0000000..1723ddb --- /dev/null +++ b/example/protein-protein/default.ini @@ -0,0 +1,59 @@ +; parameters for simulation +[simulation] +; input pose process method: +; input - just use input pose to calculation +; em - run a simple energy minimizaion for the input poses +; md - run a md simulation for the input poses +mode = em + +; simulation box type: triclinic, cubic, dodecahedron, octahedron +boxtype = triclinic + +; Distance between the solute and the simulation box +boxsize = 0.9 + +; Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration +conc = 0.15 + +; number of md simulation steps +nsteps = 500 + +; number of equilibrium simulation(nvt, npt) steps +eqsteps = 50 + +; number of structure to save for the md simulation +nframe = 10 + +; protein forcefield (gromacs engine) +proteinforcefield = amber03 + +; ligand forcefield (acpype engine): gaff, gaff2 +ligandforcefield = gaff +; ligand charge method: bcc, gas +; eem Assign Electronegativity Equilization Method (EEM) atomic partial charges. Bultinck B3LYP/6-31G*/MPA +; eem2015ba Assign Electronegativity Equilization Method (EEM) atomic partial charges. Cheminf B3LYP/6-311G/AIM +; eem2015bm Assign Electronegativity Equilization Method (EEM) atomic partial charges. Cheminf B3LYP/6-311G/MPA +; eem2015bn Assign Electronegativity Equilization Method (EEM) atomic partial charges. Cheminf B3LYP/6-311G/NPA +; eem2015ha Assign Electronegativity Equilization Method (EEM) atomic partial charges. Cheminf HF/6-311G/AIM +; eem2015hm Assign Electronegativity Equilization Method (EEM) atomic partial charges. Cheminf HF/6-311G/MPA +; eem2015hn Assign Electronegativity Equilization Method (EEM) atomic partial charges. Cheminf HF/6-311G/NPA +; gas/gasteiger Assign Gasteiger-Marsili sigma partial charges +; mmff94 Assign MMFF94 partial charges +; qeq Assign QEq (charge equilibration) partial charges (Rappe and Goddard, 1991) +; qtpie Assign QTPIE (charge transfer, polarization and equilibration) partial charges (Chen and Martinez, 2007) +; bcc Assign Am1-BCC atomic partial charge. +ligandCharge = bcc + + +; parameters for PBSA/GBSA calculation, support all the gmx_MMPBSA parameters +[GBSA] +; calculation name +sys_name = GBSA + +; calculation mode, Separated by commas. gb,pb,decomposition +modes = gb + +; best parameters for PBSA/GBSA calculations obtained from Wang, Ercheng, et al. Chemical reviews 119.16 (2019): 9478-9508. +igb = 2 +indi = 4.0 +exdi = 80.0 diff --git a/example/protein-protein/run.sh b/example/protein-protein/run.sh new file mode 100644 index 0000000..9a7d4c3 --- /dev/null +++ b/example/protein-protein/run.sh @@ -0,0 +1,10 @@ +unigbsa-pipeline -i 1vf6_REC.pdb -l 1vf6_LIG.pdb -c default.ini +# 10/16/2024 16:32:16 PM - INFO - Build protein topology. +# 10/16/2024 16:32:17 PM - INFO - Build ligand topology: 1vf6_LIG +# 10/16/2024 16:32:18 PM - INFO - Running energy minimization: 1vf6_LIG +# 10/16/2024 16:32:20 PM - INFO - Run the MMPB(GB)SA. +# 10/16/2024 16:32:28 PM - INFO - Clean the results. +# ================================================================================ +# Results: Energy.csv Dec.csv +# Frames mode delta_G(kcal/mole) +# 1 gb -57.3575 diff --git a/tests/test_pipline.py b/tests/test_pipline.py index 231af9e..839cc37 100644 --- a/tests/test_pipline.py +++ b/tests/test_pipline.py @@ -8,10 +8,12 @@ TEST_EM_CONFIG = os.path.dirname(os.path.abspath(__file__)) + '/config/em.ini' TEST_MD_CONFIG = os.path.dirname(os.path.abspath(__file__)) + '/config/md.ini' + + class TestPipline(unittest.TestCase): def setUpClass(): warnings.simplefilter('ignore', ResourceWarning) - + def base(self, pdbfile, ligandfile): pdbfile = os.path.abspath(pdbfile) ligandfile = os.path.abspath(ligandfile) @@ -65,6 +67,10 @@ def test_md(self): ligandfiles = ['../example/1ceb/1ceb_ligand.sdf'] self.pipeline_md(pdbfile, ligandfiles) + def test_protein_protein(self): + pdbfile = '../example/protein-protein/1vf6_REC.pdb' + ligandfiles = ['../example/protein-protein/1vf6_LIG.pdb'] + self.pipeline_minima(pdbfile, ligandfiles) if __name__ == "__main__": unittest.main() diff --git a/unigbsa/pipeline.py b/unigbsa/pipeline.py index 429ce08..9d00d73 100644 --- a/unigbsa/pipeline.py +++ b/unigbsa/pipeline.py @@ -53,6 +53,7 @@ def traj_pipeline(complexfile, trajfile, topolfile, indexfile, pbsaParas=None, m print('%6d %4s %18.4f '%(irow['Frames'], irow['mode'], irow['TOTAL'])) return delta_G + def base_pipeline(receptorfile, ligandfiles, paras, nt=1, mmpbsafile=None, outfile='BindingEnergy.csv', validate=False, verbose=False): """ This function takes a receptorfile and ligandfile, and build a complex.pdb and complex.top file @@ -68,7 +69,7 @@ def base_pipeline(receptorfile, ligandfiles, paras, nt=1, mmpbsafile=None, outfi receptorfile = os.path.abspath(receptorfile) logging.info('Build protein topology.') receptor = build_protein(receptorfile, forcefield=simParas['proteinforcefield']) - + cwd = os.getcwd() df = None ligandnames = [] @@ -88,7 +89,7 @@ def base_pipeline(receptorfile, ligandfiles, paras, nt=1, mmpbsafile=None, outfi topfile = 'complex.top' logging.info('Build ligand topology: %s'%ligandName) try: - build_topol(receptor, ligandfile, outpdb=grofile, outtop=topfile, ligandforce=simParas['ligandforcefield'], charge_method=simParas['ligandCharge'], nt=nt) + indexfile = build_topol(receptor, ligandfile, outpdb=grofile, outtop=topfile, ligandforce=simParas['ligandforcefield'], charge_method=simParas['ligandCharge'], nt=nt) except Exception as e: if len(ligandfiles)==1: traceback.print_exc() @@ -96,7 +97,8 @@ def base_pipeline(receptorfile, ligandfiles, paras, nt=1, mmpbsafile=None, outfi dl = d logging.warning('Failed to generate forcefield for ligand: %s'%ligandName) - indexfile = generate_index_file(grofile) + if not os.path.exists(indexfile): + indexfile = generate_index_file(grofile) if statu == 'S': try: @@ -136,9 +138,9 @@ def single(arg): if len(ligandfiles) == 1: logging.info('Build ligand topology: %s' % ligandName) try: - build_topol(receptor, ligandfile, outpdb=grofile, outtop=topfile, - ligandforce=simParas['ligandforcefield'], - charge_method=simParas['ligandCharge'], nt=nt) + indexfile = build_topol(receptor, ligandfile, outpdb=grofile, outtop=topfile, + ligandforce=simParas['ligandforcefield'], + charge_method=simParas['ligandCharge'], nt=nt) except Exception as e: statu = 'F_top' if len(ligandfiles) == 1: @@ -169,7 +171,8 @@ def single(arg): statu = 'F_md' if statu == 'S': try: - indexfile = generate_index_file(grofile) + if not os.path.exists(indexfile): + indexfile = generate_index_file(grofile) d1 = traj_pipeline(grofile, trajfile=grofile, topolfile=topfile, indexfile=indexfile, pbsaParas=pbsaParas, mmpbsafile=mmpbsafile, verbose=verbose, nt=nt, input_pdb=receptorfile) except: if len(ligandfiles) == 1: @@ -247,11 +250,10 @@ def md_pipeline(receptorfile, ligandfiles, paras, mmpbsafile=None, nt=1, outfile topfile = 'complex.top' xtcfile = 'traj_com.xtc' logging.info('Build ligand topology: %s'%ligandName) - build_topol(receptor, ligandfile, outpdb=grofile, outtop=topfile, ligandforce=simParas['ligandforcefield'], charge_method=simParas['ligandCharge'], nt=nt) + indexfile = build_topol(receptor, ligandfile, outpdb=grofile, outtop=topfile, ligandforce=simParas['ligandforcefield'], charge_method=simParas['ligandCharge'], nt=nt) logging.info('Running simulation: %s'%ligandName) engine = GMXEngine() - mdgro, mdxtc, outtop = engine.run_to_md(grofile, topfile, boxtype=simParas['boxtype'], boxsize=simParas['boxsize'], conc=simParas['conc'], nsteps=simParas['nsteps'], nframe=simParas['nframe'], eqsteps=simParas['eqsteps'], nt=nt) cmd = '%s editconf -f %s -o %s -resnr 1 >/dev/null 2>&1'%(GMXEXE, mdgro, grofile) @@ -263,7 +265,8 @@ def md_pipeline(receptorfile, ligandfiles, paras, mmpbsafile=None, nt=1, outfile shutil.copy(mdxtc, xtcfile) #logging.info('Running GBSA: %s'%ligandName) - indexfile = generate_index_file(grofile) + if not os.path.exists(indexfile): + indexfile = generate_index_file(grofile) if 'startframe' not in pbsaParas: pbsaParas["startframe"] = 2 deltaG = traj_pipeline(grofile, trajfile=xtcfile, topolfile=topfile, indexfile=indexfile, pbsaParas=pbsaParas, mmpbsafile=mmpbsafile, nt=nt, verbose=verbose, input_pdb=receptorfile) @@ -284,7 +287,7 @@ def md_pipeline(receptorfile, ligandfiles, paras, mmpbsafile=None, nt=1, outfile def main(args=None): parser = argparse.ArgumentParser(description='MM/GB(PB)SA Calculation. Version: %s'%__version__) parser.add_argument('-i', dest='receptor', help='Input protein file in pdb format.', required=True) - parser.add_argument('-l', dest='ligand', help='Ligand files to calculate binding energy for.', nargs='+', default=None) + parser.add_argument('-l', dest='ligand', help='Ligand files to calculate binding energy. For small molecular, please use format of sdf or mol, for protein ligand, please use format of pdb.', nargs='+', default=None) parser.add_argument('-c', dest='config', help='Config file, default: %s'%DEFAULT_CONFIGURE_FILE, default=DEFAULT_CONFIGURE_FILE) parser.add_argument('-d', dest='ligdir', help='Directory containing many ligand files. file format: .mol or .sdf', default=None) parser.add_argument('-f', dest='pbsafile', help='gmx_MMPBSA input file. default=None', default=None) @@ -297,12 +300,12 @@ def main(args=None): args = parser.parse_args(args) receptor, ligands, conf, ligdir, outfile, decomposition, nt, verbose = args.receptor, args.ligand, args.config, args.ligdir, args.outfile, args.decomp, args.threads, args.verbose - + if ligands is None: ligands = [] if ligdir: for fileName in os.listdir(ligdir): - if fileName.endswith(('mol','sdf')): + if fileName.endswith(('mol', 'sdf')): ligands.append(os.path.join(ligdir, fileName)) if len(ligands)==0: raise Exception('No ligand files found.') diff --git a/unigbsa/simulation/mdrun.py b/unigbsa/simulation/mdrun.py index d3e2514..73972dc 100644 --- a/unigbsa/simulation/mdrun.py +++ b/unigbsa/simulation/mdrun.py @@ -1,7 +1,7 @@ import os import shutil from unigbsa.settings import GMXEXE, MDPFILESDIR, OMP_NUM_THREADS -from unigbsa.utils import generate_index_file, process_pbc +from unigbsa.utils import generate_index_file_from_topol, process_pbc from unigbsa.simulation.utils import write_position_restrain class BaseObject(object): @@ -447,21 +447,20 @@ def run_to_md(self, pdbfile, topfile, rundir=None, boxtype='triclinic', boxsize= cwd = os.getcwd() os.chdir(rundir) mdgro, mdxtc = self.gmx_md(nptpdb, topfile, mdpfile=os.path.join(MDPFILESDIR, 'md.mdp'), nsteps=nsteps, nframe=nframe, nt=nt) - indexfile = generate_index_file(mdgro, pbc=True) + indexfile = generate_index_file_from_topol(topfile) mdxtcpbc = process_pbc(mdxtc, 'md.tpr', indexfile=indexfile, logfile=self.gmxlog) mdgropbc = process_pbc(mdgro, 'md.tpr', indexfile=indexfile, logfile=self.gmxlog) mdgro, mdxtc, topfile = os.path.abspath(mdgropbc), os.path.abspath(mdxtcpbc), os.path.abspath(topfile) os.chdir(cwd) return mdgro, mdxtc, topfile - def clean(self, pdbfile=None, rundir=None): """ If you pass a directory to the function, it will delete the directory. If you don't pass a directory, it will delete the file - + Args: pdbfile: the name of the PDB file to be cleaned rundir: the directory where the simulation will be run. diff --git a/unigbsa/simulation/topology.py b/unigbsa/simulation/topology.py index 5153943..3a0fb15 100644 --- a/unigbsa/simulation/topology.py +++ b/unigbsa/simulation/topology.py @@ -10,7 +10,7 @@ from unigbsa.simulation.mdrun import GMXEngine from unigbsa.simulation.utils import convert_format, guess_filetype, fix_insertions from unigbsa.simulation.utils import assign_partial_charge, write_position_restrain -from unigbsa.simulation.utils import obtain_net_charge +from unigbsa.simulation.utils import obtain_net_charge, gen_index_for_gbsa def build_lignad(ligandfile, forcefield="gaff2", charge_method="bcc", engine="acpype", verbose=False, outtop=None, outcoord=None, molname='MOL', itpfile=None, sqm_opt=True, nt=1): """ @@ -31,7 +31,7 @@ def build_lignad(ligandfile, forcefield="gaff2", charge_method="bcc", engine="ac ligandfile = os.path.abspath(ligandfile) ligandName = os.path.split(ligandfile)[-1][:-4]+'.TOP' filetype = guess_filetype(ligandfile) - acceptFileTypes = ('pdb', 'mol2', 'mol') + acceptFileTypes = ('mol2', 'mol') acpype_charge_methods = ['gas', 'bcc'] if charge_method not in acpype_charge_methods: @@ -39,7 +39,7 @@ def build_lignad(ligandfile, forcefield="gaff2", charge_method="bcc", engine="ac charge_method = 'user' elif filetype != 'mol': ligandfile = convert_format(ligandfile, filetype) - if not os.path.exists(ligandName): + if not os.path.exists(ligandName): os.mkdir(ligandName) charge = obtain_net_charge(ligandfile) cwd = os.getcwd() @@ -145,12 +145,12 @@ def build_protein_tleap(pdbfile, forcefield='', outtop=None, outcoor=None): def build_protein(pdbfile, forcefield='amber99sb-ildn', outtop=None, outcoord=None): """ Build a protein topology and coordinate file from a PDB file - + Args: pdbfile: The name of the PDB file to be used as input. forcefield: The forcefield to use. Options are 'amber03', 'amber94', 'amber96', 'amber99', 'amber99sb', 'amber99sb-ildn', 'amber99sb-star', 'amber14sb'. Defaults to amber99sb-ildn - + Returns: a tuple of two objects: a topology object and a Structure object. """ @@ -177,7 +177,7 @@ def build_protein(pdbfile, forcefield='amber99sb-ildn', outtop=None, outcoord=No print(cmd) os.system('tail -n 50 gromacs.log') raise Exception('ERROR run gmx! see the log file for details %s'%os.path.abspath("gromacs.log")) - + engine = GMXEngine() boxpdb = engine.gmx_box('1-pdb2gmx.gro', boxtype='triclinic', boxsize=0.9) #solpdb = engine.gmx_solvate(boxpdb, 'topol.top', maxsol=5) @@ -214,9 +214,13 @@ def build_topol(receptor, ligand, outpdb, outtop, proteinforce='amber99sb-ildn', prottop, protgro = build_protein(receptor, forcefield=proteinforce) else: prottop, protgro = receptor - + indexfile = 'index.ndx' if isinstance(ligand, str): - moltop, molgro = build_lignad(ligand, forcefield=ligandforce, charge_method=charge_method, nt=nt, verbose=verbose) + if ligand.endswith('.pdb'): + moltop, molgro = build_protein(ligand, forcefield=proteinforce) + gen_index_for_gbsa(prottop, moltop, indexfile) + else: + moltop, molgro = build_lignad(ligand, forcefield=ligandforce, charge_method=charge_method, nt=nt, verbose=verbose) elif ligand: moltop, molgro = ligand @@ -225,6 +229,7 @@ def build_topol(receptor, ligand, outpdb, outtop, proteinforce='amber99sb-ildn', else: systop = moltop + prottop sysgro = molgro + protgro + systop.write(outtop) sysgro.write_pdb(outpdb) newlines = [] @@ -260,8 +265,9 @@ def build_topol(receptor, ligand, outpdb, outtop, proteinforce='amber99sb-ildn', for k,v in atomtypes.items(): if k not in mtypes: fw.write(v+'\n') - + write_position_restrain(outtop) + return indexfile def main(): pdbfile, ligandfile = sys.argv[1], sys.argv[2] diff --git a/unigbsa/simulation/utils.py b/unigbsa/simulation/utils.py index 7415e72..19a8695 100644 --- a/unigbsa/simulation/utils.py +++ b/unigbsa/simulation/utils.py @@ -496,3 +496,26 @@ def ligand_validate(sdfile, outfile=None): return outfile else: return sdfile + + +def gen_index_for_gbsa(rec, lig, outfile='index.ndx'): + lig_atoms, rec_atoms = 0, 0 + for key, (mol, _) in rec.molecules.items(): + if key.startswith(('MOL', 'protein', 'system', 'Protein')): + rec_atoms += len(mol.atoms) + for key, (mol, _) in lig.molecules.items(): + if key.startswith(('MOL', 'protein', 'system', 'Protein')): + lig_atoms += len(mol.atoms) + + atom_dict = { + 'System': (1, lig_atoms+rec_atoms+1), + 'ligand': (1, lig_atoms+1), + 'receptor': (lig_atoms+1, rec_atoms+lig_atoms+1) + } + with open(outfile, 'w') as fw: + for k, (s, e) in atom_dict.items(): + fw.write(f'\n[ {k} ]\n') + for i, ndx in enumerate(range(s, e)): + fw.write(str(ndx) + ' ') + if i != 0 and i % 10 == 0: + fw.write('\n') diff --git a/unigbsa/utils.py b/unigbsa/utils.py index 949801d..c3f4846 100644 --- a/unigbsa/utils.py +++ b/unigbsa/utils.py @@ -1,7 +1,8 @@ -from email.policy import default import os import shutil import configparser + +import parmed as pmd from unigbsa.settings import logging, GMXEXE, DEFAULT_CONFIGURE_FILE def obtain_id_from_index(indexFile): @@ -99,6 +100,67 @@ def generate_index_file(complexfile, pbc=False): indexfile = os.path.abspath('index.ndx') return indexfile + +def generate_index_file_from_topol(topolfile): + """ + Generate index file for the complex file + Args: + complexfile: The name of the complex file. + Returns: + The index file is being returned. + """ + structure_contents = [] + with open(topolfile) as fr: + current_section = None + for line in fr: + line = line.strip() + if not line or line.startswith(';'): + continue + if line[0] == '[': + current_section = line[1:-1].strip() + elif current_section == 'molecules': + name, num = line.split() + num = int(num) + structure_contents.append((name, num)) + top = pmd.load_file(topolfile) + atoms_dict = { + 'System': [], + 'output': [], + 'Ions': [], + 'Water': [], + 'Water_and_ions': [] + } + atom_index = 1 + for i, (name, num) in enumerate(structure_contents): + molecule = top.molecules[name][0] + n_atoms = len(molecule.atoms) * num + indexs = list(range(atom_index, atom_index+n_atoms)) + atom_index = atom_index + n_atoms + atoms_dict[name] = indexs + if i == 0: + atoms_dict['center'] = indexs + if name.startswith(('system', 'protein', 'MOL')): + atoms_dict['output'].extend(indexs) + elif name == 'SOL': + atoms_dict['Water'].extend(indexs) + atoms_dict['Water_and_ions'].extend(indexs) + elif name in ['NA', 'CL']: + atoms_dict['Ions'].extend(indexs) + atoms_dict['Water_and_ions'].extend(indexs) + atoms_dict['System'].extend(indexs) + + with open('index.ndx', 'w') as fw: + for key, indexs in atoms_dict.items(): + fw.write(f'\n[ {key} ]\n') + for i, index in enumerate(indexs): + if i != 0 and i % 15 == 0: + fw.write('\n') + fw.write(str(index) + ' ') + + indexfile = os.path.abspath('index.ndx') + return indexfile + + def process_pbc(trajfile, tprfile, indexfile, outfile=None, logfile="/dev/null"): fname = os.path.split(trajfile)[-1][:-4] suffix = os.path.split(trajfile)[-1][-4:] diff --git a/unigbsa/version.py b/unigbsa/version.py index 4301ba4..793a471 100644 --- a/unigbsa/version.py +++ b/unigbsa/version.py @@ -1,2 +1,2 @@ -__version__="0.1.6" +__version__="0.1.7"