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bcif file segids start from 1 instead of old 0 in PDB
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@stefdoerr
stefdoerr committed Jul 17, 2024
1 parent 63219f0 commit 4d014bf
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Showing 7 changed files with 4,628 additions and 4,630 deletions.
572 changes: 285 additions & 287 deletions test-amber-build/dna/1BNA/input.pdb
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3,266 changes: 1,633 additions & 1,633 deletions test-amber-build/nopp/3PTB/input.pdb
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3,392 changes: 1,696 additions & 1,696 deletions test-amber-build/parameterize-cif/build/input.pdb
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522 changes: 261 additions & 261 deletions test-amber-build/peptide-cap/6A5J/input.pdb
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32 changes: 16 additions & 16 deletions test-amber-build/pp/3PTB/input.pdb
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Original file line number Diff line number Diff line change
Expand Up @@ -603,7 +603,7 @@ ATOM 601 CB LYS A 44 3.710 18.951 33.874 1.00 15.64 P0 C
ATOM 602 CG LYS A 44 2.944 19.023 32.542 0.00 0.00 P0 C
ATOM 603 CD LYS A 44 1.722 19.937 32.645 0.00 0.00 P0 C
ATOM 604 CE LYS A 44 0.811 19.461 33.778 0.00 0.00 P0 C
ATOM 605 NZ LYS A 44 -0.277 20.417 33.972 0.00 0.00 P0 N1+
ATOM 605 NZ LYS A 44 -0.277 20.417 33.972 0.00 0.00 P0 N
ATOM 606 H LYS A 44 6.284 17.495 32.959 1.00 0.00 P0 H
ATOM 607 HA LYS A 44 5.426 20.237 33.541 1.00 0.00 P0 H
ATOM 608 HB2 LYS A 44 3.634 18.031 34.231 1.00 0.00 P0 H
Expand Down Expand Up @@ -697,7 +697,7 @@ ATOM 695 CD ARG A 50 -4.513 9.035 37.853 1.00 12.24 P0 C
ATOM 696 NE ARG A 50 -4.645 9.810 39.113 1.00 12.24 P0 N
ATOM 697 CZ ARG A 50 -5.803 10.025 39.757 1.00 12.24 P0 C
ATOM 698 NH1 ARG A 50 -7.019 9.710 39.234 1.00 12.24 P0 N
ATOM 699 NH2 ARG A 50 -5.734 10.550 40.966 1.00 12.24 P0 N1+
ATOM 699 NH2 ARG A 50 -5.734 10.550 40.966 1.00 12.24 P0 N
ATOM 700 H ARG A 50 -0.623 7.823 35.807 1.00 0.00 P0 H
ATOM 701 HA ARG A 50 -1.823 6.065 37.903 1.00 0.00 P0 H
ATOM 702 HB2 ARG A 50 -3.298 7.492 35.946 1.00 0.00 P0 H
Expand Down Expand Up @@ -991,7 +991,7 @@ ATOM 989 CB LYS A 70 13.623 11.645 38.785 1.00 14.92 P0 C
ATOM 990 CG LYS A 70 14.692 11.924 37.728 1.00 24.22 P0 C
ATOM 991 CD LYS A 70 16.039 11.275 38.095 0.00 0.00 P0 C
ATOM 992 CE LYS A 70 15.896 9.761 38.324 0.00 0.00 P0 C
ATOM 993 NZ LYS A 70 16.438 9.408 39.646 0.00 0.00 P0 N1+
ATOM 993 NZ LYS A 70 16.438 9.408 39.646 0.00 0.00 P0 N
ATOM 994 H LYS A 70 10.718 10.946 39.295 1.00 0.00 P0 H
ATOM 995 HA LYS A 70 12.319 13.369 38.933 1.00 0.00 P0 H
ATOM 996 HB2 LYS A 70 14.017 11.850 39.696 1.00 0.00 P0 H
Expand Down Expand Up @@ -1308,7 +1308,7 @@ ATOM 1306 CB LYS A 90 12.330 7.681 37.963 1.00 9.20 P0 C
ATOM 1307 CG LYS A 90 12.578 6.496 38.954 1.00 15.55 P0 C
ATOM 1308 CD LYS A 90 13.943 6.599 39.630 1.00 15.55 P0 C
ATOM 1309 CE LYS A 90 14.326 5.288 40.336 1.00 15.55 P0 C
ATOM 1310 NZ LYS A 90 15.693 5.417 40.891 1.00 15.55 P0 N1+
ATOM 1310 NZ LYS A 90 15.693 5.417 40.891 1.00 15.55 P0 N
ATOM 1311 H LYS A 90 11.008 9.556 36.450 1.00 0.00 P0 H
ATOM 1312 HA LYS A 90 10.832 6.642 36.903 1.00 0.00 P0 H
ATOM 1313 HB2 LYS A 90 12.984 7.616 37.251 1.00 0.00 P0 H
Expand Down Expand Up @@ -1349,7 +1349,7 @@ ATOM 1347 CB LYS A 92 7.561 7.824 44.440 1.00 17.95 P0 C
ATOM 1348 CG LYS A 92 7.861 9.315 44.621 1.00 23.79 P0 C
ATOM 1349 CD LYS A 92 6.773 10.004 45.463 0.00 0.00 P0 C
ATOM 1350 CE LYS A 92 7.032 11.512 45.632 0.00 0.00 P0 C
ATOM 1351 NZ LYS A 92 5.978 12.107 46.463 0.00 0.00 P0 N1+
ATOM 1351 NZ LYS A 92 5.978 12.107 46.463 0.00 0.00 P0 N
ATOM 1352 H LYS A 92 7.249 7.518 41.902 1.00 0.00 P0 H
ATOM 1353 HA LYS A 92 9.540 7.528 43.587 1.00 0.00 P0 H
ATOM 1354 HB2 LYS A 92 6.687 7.737 43.983 1.00 0.00 P0 H
Expand Down Expand Up @@ -1459,7 +1459,7 @@ ATOM 1457 CD ARG A 100 -4.650 -5.321 37.317 0.00 0.00 P0 C
ATOM 1458 NE ARG A 100 -4.445 -6.024 38.600 0.00 0.00 P0 N
ATOM 1459 CZ ARG A 100 -4.843 -5.750 39.844 0.00 0.00 P0 C
ATOM 1460 NH1 ARG A 100 -4.477 -6.538 40.829 0.00 0.00 P0 N
ATOM 1461 NH2 ARG A 100 -5.488 -4.656 40.170 0.00 0.00 P0 N1+
ATOM 1461 NH2 ARG A 100 -5.488 -4.656 40.170 0.00 0.00 P0 N
ATOM 1462 H ARG A 100 -2.864 -7.645 35.332 1.00 0.00 P0 H
ATOM 1463 HA ARG A 100 -3.926 -6.126 33.045 1.00 0.00 P0 H
ATOM 1464 HB2 ARG A 100 -5.151 -4.920 34.804 1.00 0.00 P0 H
Expand Down Expand Up @@ -1810,7 +1810,7 @@ ATOM 1808 CB LYS A 126 -14.433 15.224 17.361 1.00 19.22 P0 C
ATOM 1809 CG LYS A 126 -15.593 14.476 18.031 1.00 16.57 P0 C
ATOM 1810 CD LYS A 126 -16.128 13.305 17.184 0.00 0.00 P0 C
ATOM 1811 CE LYS A 126 -17.028 12.381 18.025 0.00 0.00 P0 C
ATOM 1812 NZ LYS A 126 -17.339 11.157 17.278 0.00 0.00 P0 N1+
ATOM 1812 NZ LYS A 126 -17.339 11.157 17.278 0.00 0.00 P0 N
ATOM 1813 H LYS A 126 -12.346 13.971 18.933 1.00 0.00 P0 H
ATOM 1814 HA LYS A 126 -13.799 13.537 16.360 1.00 0.00 P0 H
ATOM 1815 HB2 LYS A 126 -14.054 15.853 18.004 1.00 0.00 P0 H
Expand Down Expand Up @@ -1968,7 +1968,7 @@ ATOM 1966 CB LYS A 137 -10.081 5.256 22.161 1.00 10.20 P0 C
ATOM 1967 CG LYS A 137 -11.618 5.407 21.966 1.00 16.74 P0 C
ATOM 1968 CD LYS A 137 -12.482 5.336 23.156 1.00 16.74 P0 C
ATOM 1969 CE LYS A 137 -13.936 5.281 22.683 1.00 16.74 P0 C
ATOM 1970 NZ LYS A 137 -14.863 5.116 23.812 0.00 0.00 P0 N1+
ATOM 1970 NZ LYS A 137 -14.863 5.116 23.812 0.00 0.00 P0 N
ATOM 1971 H LYS A 137 -8.640 5.027 24.592 1.00 0.00 P0 H
ATOM 1972 HA LYS A 137 -10.278 3.255 22.851 1.00 0.00 P0 H
ATOM 1973 HB2 LYS A 137 -9.763 6.051 22.687 1.00 0.00 P0 H
Expand Down Expand Up @@ -2019,7 +2019,7 @@ ATOM 2017 CB LYS A 140 -5.145 -1.675 14.165 1.00 13.01 P0 C
ATOM 2018 CG LYS A 140 -5.314 -2.584 15.388 1.00 17.59 P0 C
ATOM 2019 CD LYS A 140 -5.716 -3.997 14.899 1.00 17.59 P0 C
ATOM 2020 CE LYS A 140 -5.942 -5.034 16.030 1.00 17.59 P0 C
ATOM 2021 NZ LYS A 140 -7.174 -4.732 16.769 0.00 0.00 P0 N1+
ATOM 2021 NZ LYS A 140 -7.174 -4.732 16.769 0.00 0.00 P0 N
ATOM 2022 H LYS A 140 -6.732 0.310 15.023 1.00 0.00 P0 H
ATOM 2023 HA LYS A 140 -3.845 -0.277 15.140 1.00 0.00 P0 H
ATOM 2024 HB2 LYS A 140 -6.021 -1.583 13.721 1.00 0.00 P0 H
Expand Down Expand Up @@ -2158,7 +2158,7 @@ ATOM 2156 CB LYS A 150 9.679 13.223 3.883 1.00 16.65 P0 C
ATOM 2157 CG LYS A 150 10.311 12.801 5.222 0.00 0.00 P0 C
ATOM 2158 CD LYS A 150 11.821 12.534 5.105 0.00 0.00 P0 C
ATOM 2159 CE LYS A 150 12.443 12.203 6.474 0.00 0.00 P0 C
ATOM 2160 NZ LYS A 150 13.812 11.706 6.302 0.00 0.00 P0 N1+
ATOM 2160 NZ LYS A 150 13.812 11.706 6.302 0.00 0.00 P0 N
ATOM 2161 H LYS A 150 7.752 11.332 4.088 1.00 0.00 P0 H
ATOM 2162 HA LYS A 150 8.186 14.088 4.876 1.00 0.00 P0 H
ATOM 2163 HB2 LYS A 150 9.783 12.492 3.243 1.00 0.00 P0 H
Expand Down Expand Up @@ -2451,7 +2451,7 @@ ATOM 2449 CB LYS A 171 -8.311 6.065 11.205 1.00 16.81 P0 C
ATOM 2450 CG LYS A 171 -9.692 5.466 10.836 1.00 18.60 P0 C
ATOM 2451 CD LYS A 171 -9.652 3.933 10.572 1.00 18.60 P0 C
ATOM 2452 CE LYS A 171 -11.054 3.363 10.271 0.00 0.00 P0 C
ATOM 2453 NZ LYS A 171 -10.988 1.909 10.072 0.00 0.00 P0 N1+
ATOM 2453 NZ LYS A 171 -10.988 1.909 10.072 0.00 0.00 P0 N
ATOM 2454 H LYS A 171 -8.356 8.783 9.762 1.00 0.00 P0 H
ATOM 2455 HA LYS A 171 -9.046 7.619 12.400 1.00 0.00 P0 H
ATOM 2456 HB2 LYS A 171 -7.728 6.013 10.417 1.00 0.00 P0 H
Expand Down Expand Up @@ -2641,7 +2641,7 @@ ATOM 2639 CB LYS A 187 8.745 -4.226 20.321 1.00 11.68 P0 C
ATOM 2640 CG LYS A 187 9.461 -5.538 20.828 1.00 20.82 P0 C
ATOM 2641 CD LYS A 187 8.898 -6.839 20.237 0.00 0.00 P0 C
ATOM 2642 CE LYS A 187 9.521 -8.092 20.874 0.00 0.00 P0 C
ATOM 2643 NZ LYS A 187 8.872 -9.293 20.334 0.00 0.00 P0 N1+
ATOM 2643 NZ LYS A 187 8.872 -9.293 20.334 0.00 0.00 P0 N
ATOM 2644 H LYS A 187 5.893 -4.686 19.802 1.00 0.00 P0 H
ATOM 2645 HA LYS A 187 7.648 -4.149 22.136 1.00 0.00 P0 H
ATOM 2646 HB2 LYS A 187 8.476 -4.377 19.400 1.00 0.00 P0 H
Expand Down Expand Up @@ -2838,7 +2838,7 @@ ATOM 2836 CB LYS A 201 -7.494 14.254 3.448 1.00 15.08 P0 C
ATOM 2837 CG LYS A 201 -7.066 13.566 2.151 1.00 19.72 P0 C
ATOM 2838 CD LYS A 201 -7.896 14.098 0.973 0.00 0.00 P0 C
ATOM 2839 CE LYS A 201 -7.488 13.470 -0.367 0.00 0.00 P0 C
ATOM 2840 NZ LYS A 201 -8.294 14.065 -1.439 0.00 0.00 P0 N1+
ATOM 2840 NZ LYS A 201 -8.294 14.065 -1.439 0.00 0.00 P0 N
ATOM 2841 H LYS A 201 -8.105 14.972 5.852 1.00 0.00 P0 H
ATOM 2842 HA LYS A 201 -6.575 12.842 4.789 1.00 0.00 P0 H
ATOM 2843 HB2 LYS A 201 -8.429 13.998 3.645 1.00 0.00 P0 H
Expand Down Expand Up @@ -2874,7 +2874,7 @@ ATOM 2872 CB LYS A 203 -2.466 15.965 7.833 1.00 15.43 P0 C
ATOM 2873 CG LYS A 203 -2.266 17.171 6.858 1.00 27.47 P0 C
ATOM 2874 CD LYS A 203 -0.753 17.464 6.597 1.00 27.47 P0 C
ATOM 2875 CE LYS A 203 -0.540 18.817 5.851 1.00 27.47 P0 C
ATOM 2876 NZ LYS A 203 0.890 19.214 5.733 1.00 27.47 P0 N1+
ATOM 2876 NZ LYS A 203 0.890 19.214 5.733 1.00 27.47 P0 N
ATOM 2877 H LYS A 203 -3.555 13.711 6.182 1.00 0.00 P0 H
ATOM 2878 HA LYS A 203 -0.931 14.831 6.972 1.00 0.00 P0 H
ATOM 2879 HB2 LYS A 203 -3.433 15.842 7.963 1.00 0.00 P0 H
Expand Down Expand Up @@ -2968,7 +2968,7 @@ ATOM 2966 CB LYS A 209 11.857 6.925 15.400 1.00 8.39 P0 C
ATOM 2967 CG LYS A 209 12.190 5.630 14.644 1.00 21.92 P0 C
ATOM 2968 CD LYS A 209 12.870 6.022 13.317 1.00 21.92 P0 C
ATOM 2969 CE LYS A 209 12.660 4.959 12.243 1.00 21.92 P0 C
ATOM 2970 NZ LYS A 209 13.317 5.374 11.000 0.00 0.00 P0 N1+
ATOM 2970 NZ LYS A 209 13.317 5.374 11.000 0.00 0.00 P0 N
ATOM 2971 H LYS A 209 10.958 8.877 16.878 1.00 0.00 P0 H
ATOM 2972 HA LYS A 209 10.229 6.052 16.460 1.00 0.00 P0 H
ATOM 2973 HB2 LYS A 209 11.365 7.522 14.783 1.00 0.00 P0 H
Expand Down Expand Up @@ -3121,7 +3121,7 @@ ATOM 3119 CB LYS A 218 19.582 0.748 28.065 1.00 10.80 P0 C
ATOM 3120 CG LYS A 218 18.447 -0.063 27.395 1.00 17.60 P0 C
ATOM 3121 CD LYS A 218 18.969 -1.410 26.855 0.00 0.00 P0 C
ATOM 3122 CE LYS A 218 20.364 -1.301 26.204 0.00 0.00 P0 C
ATOM 3123 NZ LYS A 218 20.345 -0.445 25.011 0.00 0.00 P0 N1+
ATOM 3123 NZ LYS A 218 20.345 -0.445 25.011 0.00 0.00 P0 N
ATOM 3124 H LYS A 218 18.323 2.771 27.100 1.00 0.00 P0 H
ATOM 3125 HA LYS A 218 18.288 1.364 29.539 1.00 0.00 P0 H
ATOM 3126 HB2 LYS A 218 20.108 1.177 27.357 1.00 0.00 P0 H
Expand Down
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