O-linked glycosylation

HADDOCK
1

Dear Bonvin lab,

I am trying to model an O-glycosylated protein ligand binding to a protein in Haddock3 locally. My understanding is that since the O-glycan linkage is not recognised in the topo step the linkage is cut and there is an extra O added to the glycan to “complete” the molecule. I have implemented distance restraints to try and stop the sugars from flying away from the peptide backbone. But I guess haddock is constantly fighting between having overlapping atoms and the restraints. Either way the docked outputs are still doing “odd” things to the glycans. I suppose I could just add in more constraints but perhaps I am missing something?

I saw in a previous message you said that O-glycans were in the pipeline, am I correct in thinking they are not yet supported?

image
image781×443 76.8 KB

Thanks!

2

The list of supported glycans can be found at: https://rascar.science.uu.nl/haddock2.4/library

If you think your glycans should be supported, please share your input PDB.

3

Thanks for looking into this. I believe the glycans (NGA) are supported.

I cannot attach but I have copied the contents of the PDB below:

ATOM 1 N NGA B 1 6.560 0.087 -2.346 1.00 0.00 CARA N
ATOM 2 C NGA B 1 7.063 1.225 -1.818 1.00 0.00 CARA C
ATOM 3 O NGA B 1 7.959 1.880 -2.349 1.00 0.00 CARA O
ATOM 4 C1 NGA B 1 6.903 -2.025 -3.465 1.00 0.00 CARA C
ATOM 5 C2 NGA B 1 6.975 -0.530 -3.586 1.00 0.00 CARA C
ATOM 6 C3 NGA B 1 6.243 -0.024 -4.809 1.00 0.00 CARA C
ATOM 7 O3 NGA B 1 6.418 1.372 -4.983 1.00 0.00 CARA O
ATOM 8 C4 NGA B 1 6.672 -0.806 -6.033 1.00 0.00 CARA C
ATOM 9 O4 NGA B 1 8.008 -0.510 -6.410 1.00 0.00 CARA O
ATOM 10 C5 NGA B 1 6.507 -2.300 -5.779 1.00 0.00 CARA C
ATOM 11 O5 NGA B 1 7.318 -2.690 -4.662 1.00 0.00 CARA O
ATOM 12 C6 NGA B 1 6.882 -3.162 -6.964 1.00 0.00 CARA C
ATOM 13 O6 NGA B 1 6.608 -4.536 -6.712 1.00 0.00 CARA O
ATOM 14 CT NGA B 1 6.449 1.670 -0.501 1.00 0.00 CARA C
ATOM 15 HN NGA B 1 5.836 -0.404 -1.871 1.00 0.00 CARA H
ATOM 16 HO3 NGA B 1 7.353 1.559 -5.087 1.00 0.00 CARA H
ATOM 17 HO4 NGA B 1 8.599 -0.776 -5.701 1.00 0.00 CARA H
ATOM 18 HO6 NGA B 1 7.317 -4.903 -6.179 1.00 0.00 CARA H
ATOM 19 HT1 NGA B 1 6.600 0.880 0.264 1.00 0.00 CARA H
ATOM 20 HT2 NGA B 1 5.359 1.840 -0.634 1.00 0.00 CARA H
ATOM 21 HT3 NGA B 1 6.940 2.605 -0.156 1.00 0.00 CARA H
ATOM 22 H1 NGA B 1 7.656 -2.231 -2.675 1.00 0.00 CARA H
ATOM 23 H2 NGA B 1 8.018 -0.216 -3.803 1.00 0.00 CARA H
ATOM 24 H3 NGA B 1 5.157 -0.232 -4.701 1.00 0.00 CARA H
ATOM 25 H4 NGA B 1 6.049 -0.506 -6.903 1.00 0.00 CARA H
ATOM 26 H5 NGA B 1 5.442 -2.527 -5.556 1.00 0.00 CARA H
ATOM 27 H61 NGA B 1 7.967 -3.051 -7.174 1.00 0.00 CARA H
ATOM 28 H62 NGA B 1 6.298 -2.843 -7.853 1.00 0.00 CARA H
ATOM 29 N NGA B 2 7.494 -8.769 3.750 1.00 0.00 CARB N
ATOM 30 C NGA B 2 7.105 -9.281 4.941 1.00 0.00 CARB C
ATOM 31 O NGA B 2 5.983 -9.746 5.142 1.00 0.00 CARB O
ATOM 32 C1 NGA B 2 6.986 -7.478 1.752 1.00 0.00 CARB C
ATOM 33 C2 NGA B 2 6.682 -8.723 2.554 1.00 0.00 CARB C
ATOM 34 C3 NGA B 2 6.763 -9.978 1.715 1.00 0.00 CARB C
ATOM 35 O3 NGA B 2 6.381 -11.128 2.450 1.00 0.00 CARB O
ATOM 36 C4 NGA B 2 5.934 -9.822 0.464 1.00 0.00 CARB C
ATOM 37 O4 NGA B 2 4.544 -9.788 0.749 1.00 0.00 CARB O
ATOM 38 C5 NGA B 2 6.359 -8.565 -0.279 1.00 0.00 CARB C
ATOM 39 O5 NGA B 2 6.188 -7.411 0.560 1.00 0.00 CARB O
ATOM 40 C6 NGA B 2 5.572 -8.357 -1.556 1.00 0.00 CARB C
ATOM 41 O6 NGA B 2 6.075 -7.270 -2.322 1.00 0.00 CARB O
ATOM 42 CT NGA B 2 8.141 -9.260 6.052 1.00 0.00 CARB C
ATOM 43 HN NGA B 2 8.406 -8.382 3.643 1.00 0.00 CARB H
ATOM 44 HO3 NGA B 2 7.157 -11.670 2.607 1.00 0.00 CARB H
ATOM 45 HO4 NGA B 2 4.356 -9.020 1.294 1.00 0.00 CARB H
ATOM 46 HO6 NGA B 2 5.880 -6.449 -1.865 1.00 0.00 CARB H
ATOM 47 HT1 NGA B 2 8.447 -8.212 6.255 1.00 0.00 CARB H
ATOM 48 HT2 NGA B 2 9.035 -9.843 5.742 1.00 0.00 CARB H
ATOM 49 HT3 NGA B 2 7.708 -9.695 6.978 1.00 0.00 CARB H
ATOM 50 H1 NGA B 2 6.653 -6.668 2.435 1.00 0.00 CARB H
ATOM 51 H2 NGA B 2 5.613 -8.725 2.858 1.00 0.00 CARB H
ATOM 52 H3 NGA B 2 7.807 -10.117 1.361 1.00 0.00 CARB H
ATOM 53 H4 NGA B 2 6.077 -10.708 -0.191 1.00 0.00 CARB H
ATOM 54 H5 NGA B 2 7.428 -8.648 -0.571 1.00 0.00 CARB H
ATOM 55 H61 NGA B 2 4.511 -8.144 -1.303 1.00 0.00 CARB H
ATOM 56 H62 NGA B 2 5.627 -9.277 -2.176 1.00 0.00 CARB H
ATOM 57 N NGA B 3 9.538 -8.547 -4.485 1.00 0.00 CARC N
ATOM 58 C NGA B 3 8.335 -9.165 -4.463 1.00 0.00 CARC C
ATOM 59 O NGA B 3 7.370 -8.791 -5.127 1.00 0.00 CARC O
ATOM 60 C1 NGA B 3 10.783 -6.471 -4.486 1.00 0.00 CARC C
ATOM 61 C2 NGA B 3 9.872 -7.378 -5.267 1.00 0.00 CARC C
ATOM 62 C3 NGA B 3 10.422 -7.688 -6.639 1.00 0.00 CARC C
ATOM 63 O3 NGA B 3 9.508 -8.453 -7.406 1.00 0.00 CARC O
ATOM 64 C4 NGA B 3 10.817 -6.408 -7.342 1.00 0.00 CARC C
ATOM 65 O4 NGA B 3 9.687 -5.624 -7.691 1.00 0.00 CARC O
ATOM 66 C5 NGA B 3 11.770 -5.611 -6.462 1.00 0.00 CARC C
ATOM 67 O5 NGA B 3 11.129 -5.292 -5.220 1.00 0.00 CARC O
ATOM 68 C6 NGA B 3 12.243 -4.322 -7.097 1.00 0.00 CARC C
ATOM 69 O6 NGA B 3 13.207 -3.665 -6.282 1.00 0.00 CARC O
ATOM 70 CT NGA B 3 8.232 -10.379 -3.555 1.00 0.00 CARC C
ATOM 71 HN NGA B 3 10.289 -8.894 -3.929 1.00 0.00 CARC H
ATOM 72 HO3 NGA B 3 8.692 -7.957 -7.507 1.00 0.00 CARC H
ATOM 73 HO4 NGA B 3 9.229 -5.361 -6.890 1.00 0.00 CARC H
ATOM 74 HO6 NGA B 3 12.754 -3.192 -5.581 1.00 0.00 CARC H
ATOM 75 HT1 NGA B 3 8.445 -10.078 -2.507 1.00 0.00 CARC H
ATOM 76 HT2 NGA B 3 8.973 -11.146 -3.868 1.00 0.00 CARC H
ATOM 77 HT3 NGA B 3 7.205 -10.801 -3.608 1.00 0.00 CARC H
ATOM 78 H1 NGA B 3 10.135 -6.173 -3.634 1.00 0.00 CARC H
ATOM 79 H2 NGA B 3 8.931 -6.844 -5.519 1.00 0.00 CARC H
ATOM 80 H3 NGA B 3 11.366 -8.265 -6.538 1.00 0.00 CARC H
ATOM 81 H4 NGA B 3 11.316 -6.650 -8.305 1.00 0.00 CARC H
ATOM 82 H5 NGA B 3 12.683 -6.211 -6.259 1.00 0.00 CARC H
ATOM 83 H61 NGA B 3 11.377 -3.640 -7.238 1.00 0.00 CARC H
ATOM 84 H62 NGA B 3 12.704 -4.543 -8.083 1.00 0.00 CARC H
ATOM 85 N NGA B 4 13.253 -14.254 -1.445 1.00 0.00 CARD N
ATOM 86 C NGA B 4 13.836 -15.291 -2.088 1.00 0.00 CARD C
ATOM 87 O NGA B 4 13.542 -16.467 -1.881 1.00 0.00 CARD O
ATOM 88 C1 NGA B 4 12.452 -13.323 0.646 1.00 0.00 CARD C
ATOM 89 C2 NGA B 4 12.236 -14.360 -0.424 1.00 0.00 CARD C
ATOM 90 C3 NGA B 4 10.820 -14.338 -0.949 1.00 0.00 CARD C
ATOM 91 O3 NGA B 4 10.600 -15.367 -1.899 1.00 0.00 CARD O
ATOM 92 C4 NGA B 4 9.840 -14.411 0.201 1.00 0.00 CARD C
ATOM 93 O4 NGA B 4 9.852 -15.684 0.827 1.00 0.00 CARD O
ATOM 94 C5 NGA B 4 10.148 -13.315 1.213 1.00 0.00 CARD C
ATOM 95 O5 NGA B 4 11.491 -13.467 1.699 1.00 0.00 CARD O
ATOM 96 C6 NGA B 4 9.205 -13.317 2.397 1.00 0.00 CARD C
ATOM 97 O6 NGA B 4 9.413 -12.187 3.236 1.00 0.00 CARD O
ATOM 98 CT NGA B 4 14.900 -14.924 -3.110 1.00 0.00 CARD C
ATOM 99 HN NGA B 4 13.516 -13.318 -1.662 1.00 0.00 CARD H
ATOM 100 HO3 NGA B 4 10.760 -16.217 -1.482 1.00 0.00 CARD H
ATOM 101 HO4 NGA B 4 10.721 -15.839 1.205 1.00 0.00 CARD H
ATOM 102 HO6 NGA B 4 8.974 -11.425 2.849 1.00 0.00 CARD H
ATOM 103 HT1 NGA B 4 15.721 -14.370 -2.608 1.00 0.00 CARD H
ATOM 104 HT2 NGA B 4 14.457 -14.277 -3.897 1.00 0.00 CARD H
ATOM 105 HT3 NGA B 4 15.315 -15.848 -3.568 1.00 0.00 CARD H
ATOM 106 H1 NGA B 4 13.452 -13.596 1.046 1.00 0.00 CARD H
ATOM 107 H2 NGA B 4 12.291 -15.377 0.019 1.00 0.00 CARD H
ATOM 108 H3 NGA B 4 10.622 -13.360 -1.437 1.00 0.00 CARD H
ATOM 109 H4 NGA B 4 8.805 -14.281 -0.183 1.00 0.00 CARD H
ATOM 110 H5 NGA B 4 10.043 -12.319 0.731 1.00 0.00 CARD H
ATOM 111 H61 NGA B 4 9.371 -14.236 2.999 1.00 0.00 CARD H
ATOM 112 H62 NGA B 4 8.156 -13.297 2.034 1.00 0.00 CARD H
ATOM 113 N ALA B 5 -0.525 1.362 0.000 1.00 1.00 PROA N
ATOM 114 CA ALA B 5 0.000 0.000 0.000 1.00 1.00 PROA C
ATOM 115 C ALA B 5 1.520 0.000 0.000 1.00 1.00 PROA C
ATOM 116 O ALA B 5 2.144 0.812 -0.681 1.00 1.00 PROA O
ATOM 117 CB ALA B 5 -0.507 -0.774 -1.206 1.00 1.00 PROA C
ATOM 118 HA ALA B 5 -0.320 -0.476 0.915 1.00 0.00 PROA H
ATOM 119 HB1 ALA B 5 -0.186 -0.273 -2.144 1.00 0.00 PROA H
ATOM 120 HB2 ALA B 5 -1.617 -0.816 -1.189 1.00 0.00 PROA H
ATOM 121 HB3 ALA B 5 -0.093 -1.805 -1.195 1.00 0.00 PROA H
ATOM 122 HT1 ALA B 5 -0.154 1.877 0.824 1.00 0.00 PROA H
ATOM 123 HT2 ALA B 5 -1.564 1.333 0.048 1.00 0.00 PROA H
ATOM 124 HT3 ALA B 5 -0.232 1.847 -0.872 1.00 0.00 PROA H
ATOM 125 N ALA B 6 2.116 -0.911 0.764 1.00 1.00 PROA N
ATOM 126 CA ALA B 6 3.571 -1.003 0.842 1.00 1.00 PROA C
ATOM 127 C ALA B 6 4.057 -2.369 0.384 1.00 1.00 PROA C
ATOM 128 O ALA B 6 3.442 -3.387 0.694 1.00 1.00 PROA O
ATOM 129 CB ALA B 6 4.054 -0.742 2.259 1.00 1.00 PROA C
ATOM 130 HN ALA B 6 1.602 -1.566 1.312 1.00 0.00 PROA H
ATOM 131 HA ALA B 6 3.988 -0.273 0.164 1.00 0.00 PROA H
ATOM 132 HB1 ALA B 6 3.617 -1.489 2.955 1.00 0.00 PROA H
ATOM 133 HB2 ALA B 6 3.740 0.273 2.585 1.00 0.00 PROA H
ATOM 134 HB3 ALA B 6 5.161 -0.823 2.302 1.00 0.00 PROA H
ATOM 135 N THR B 7 5.182 -2.423 -0.364 1.00 1.00 PROA N
ATOM 136 CA THR B 7 5.718 -3.654 -0.916 1.00 1.00 PROA C
ATOM 137 C THR B 7 7.145 -3.787 -0.457 1.00 1.00 PROA C
ATOM 138 O THR B 7 7.784 -2.801 -0.088 1.00 1.00 PROA O
ATOM 139 CB THR B 7 5.591 -3.740 -2.434 1.00 1.00 PROA C
ATOM 140 CG2 THR B 7 4.204 -4.311 -2.794 1.00 1.00 PROA C
ATOM 141 OG1 THR B 7 5.648 -2.420 -2.987 1.00 1.00 PROA O
ATOM 142 HN THR B 7 5.705 -1.601 -0.574 1.00 0.00 PROA H
ATOM 143 HA THR B 7 5.181 -4.472 -0.459 1.00 0.00 PROA H
ATOM 144 HB THR B 7 6.422 -4.350 -2.849 1.00 0.00 PROA H
ATOM 145 HG21 THR B 7 3.404 -3.652 -2.394 1.00 0.00 PROA H
ATOM 146 HG22 THR B 7 4.084 -5.323 -2.350 1.00 0.00 PROA H
ATOM 147 HG23 THR B 7 4.095 -4.373 -3.898 1.00 0.00 PROA H
ATOM 148 N THR B 8 7.649 -5.048 -0.433 1.00 1.00 PROA N
ATOM 149 CA THR B 8 8.951 -5.405 0.085 1.00 1.00 PROA C
ATOM 150 C THR B 8 9.617 -6.358 -0.872 1.00 1.00 PROA C
ATOM 151 O THR B 8 8.957 -6.972 -1.706 1.00 1.00 PROA O
ATOM 152 CB THR B 8 8.965 -6.008 1.497 1.00 1.00 PROA C
ATOM 153 CG2 THR B 8 8.435 -4.957 2.508 1.00 1.00 PROA C
ATOM 154 OG1 THR B 8 8.379 -7.336 1.550 1.00 1.00 PROA O
ATOM 155 HN THR B 8 7.119 -5.814 -0.786 1.00 0.00 PROA H
ATOM 156 HA THR B 8 9.543 -4.502 0.082 1.00 0.00 PROA H
ATOM 157 HB THR B 8 10.017 -6.074 1.850 1.00 0.00 PROA H
ATOM 158 HG21 THR B 8 7.396 -4.665 2.245 1.00 0.00 PROA H
ATOM 159 HG22 THR B 8 9.076 -4.050 2.482 1.00 0.00 PROA H
ATOM 160 HG23 THR B 8 8.434 -5.386 3.533 1.00 0.00 PROA H
ATOM 161 N THR B 9 10.959 -6.493 -0.757 1.00 1.00 PROA N
ATOM 162 CA THR B 9 11.768 -7.358 -1.584 1.00 1.00 PROA C
ATOM 163 C THR B 9 12.761 -7.975 -0.637 1.00 1.00 PROA C
ATOM 164 O THR B 9 13.278 -7.294 0.250 1.00 1.00 PROA O
ATOM 165 CB THR B 9 12.427 -6.626 -2.768 1.00 1.00 PROA C
ATOM 166 CG2 THR B 9 13.966 -6.744 -2.864 1.00 1.00 PROA C
ATOM 167 OG1 THR B 9 11.883 -7.178 -3.974 1.00 1.00 PROA O
ATOM 168 HN THR B 9 11.466 -5.980 -0.070 1.00 0.00 PROA H
ATOM 169 HA THR B 9 11.125 -8.143 -1.954 1.00 0.00 PROA H
ATOM 170 HB THR B 9 12.206 -5.538 -2.718 1.00 0.00 PROA H
ATOM 171 HG21 THR B 9 14.262 -7.810 -2.966 1.00 0.00 PROA H
ATOM 172 HG22 THR B 9 14.435 -6.332 -1.945 1.00 0.00 PROA H
ATOM 173 HG23 THR B 9 14.333 -6.188 -3.753 1.00 0.00 PROA H
ATOM 174 N THR B 10 13.016 -9.302 -0.786 1.00 1.00 PROA N
ATOM 175 CA THR B 10 13.919 -10.041 0.070 1.00 1.00 PROA C
ATOM 176 C THR B 10 15.001 -10.679 -0.794 1.00 1.00 PROA C
ATOM 177 O THR B 10 14.684 -11.558 -1.592 1.00 1.00 PROA O
ATOM 178 CB THR B 10 13.229 -11.084 0.946 1.00 1.00 PROA C
ATOM 179 CG2 THR B 10 12.246 -10.371 1.900 1.00 1.00 PROA C
ATOM 180 OG1 THR B 10 12.530 -12.024 0.112 1.00 1.00 PROA O
ATOM 181 HN THR B 10 12.583 -9.834 -1.508 1.00 0.00 PROA H
ATOM 182 HA THR B 10 14.425 -9.322 0.697 1.00 0.00 PROA H
ATOM 183 HB THR B 10 13.986 -11.625 1.554 1.00 0.00 PROA H
ATOM 184 HG21 THR B 10 11.383 -9.969 1.327 1.00 0.00 PROA H
ATOM 185 HG22 THR B 10 12.758 -9.526 2.408 1.00 0.00 PROA H
ATOM 186 HG23 THR B 10 11.865 -11.089 2.657 1.00 0.00 PROA H
ATOM 187 N PRO B 11 16.269 -10.282 -0.695 1.00 1.00 PROA N
ATOM 188 CA PRO B 11 17.329 -10.798 -1.557 1.00 1.00 PROA C
ATOM 189 C PRO B 11 18.157 -11.881 -0.886 1.00 1.00 PROA C
ATOM 190 O PRO B 11 18.470 -11.783 0.300 1.00 1.00 PROA O
ATOM 191 CB PRO B 11 18.204 -9.586 -1.831 1.00 1.00 PROA C
ATOM 192 CG PRO B 11 18.049 -8.741 -0.613 1.00 1.00 PROA C
ATOM 193 CD PRO B 11 16.627 -8.942 -0.179 1.00 1.00 PROA C
ATOM 194 HA PRO B 11 16.904 -11.252 -2.438 1.00 0.00 PROA H
ATOM 195 HB1 PRO B 11 17.859 -9.044 -2.737 1.00 0.00 PROA H
ATOM 196 HB2 PRO B 11 19.264 -9.886 -1.974 1.00 0.00 PROA H
ATOM 197 HG1 PRO B 11 18.753 -9.065 0.183 1.00 0.00 PROA H
ATOM 198 HG2 PRO B 11 18.241 -7.672 -0.848 1.00 0.00 PROA H
ATOM 199 HD1 PRO B 11 16.537 -8.928 0.928 1.00 0.00 PROA H
ATOM 200 HD2 PRO B 11 15.957 -8.176 -0.623 1.00 0.00 PROA H
ATOM 201 N ALA B 12 18.513 -12.915 -1.643 1.00 1.00 PROA N
ATOM 202 CA ALA B 12 19.309 -14.014 -1.104 1.00 1.00 PROA C
ATOM 203 C ALA B 12 20.623 -14.157 -1.855 1.00 1.00 PROA C
ATOM 204 O ALA B 12 20.657 -14.019 -3.077 1.00 1.00 PROA O
ATOM 205 CB ALA B 12 18.540 -15.323 -1.174 1.00 1.00 PROA C
ATOM 206 HN ALA B 12 18.255 -12.986 -2.603 1.00 0.00 PROA H
ATOM 207 HA ALA B 12 19.553 -13.778 -0.079 1.00 0.00 PROA H
ATOM 208 HB1 ALA B 12 18.283 -15.559 -2.229 1.00 0.00 PROA H
ATOM 209 HB2 ALA B 12 17.599 -15.240 -0.590 1.00 0.00 PROA H
ATOM 210 HB3 ALA B 12 19.162 -16.149 -0.767 1.00 0.00 PROA H
ATOM 211 N PRO B 13 21.700 -14.432 -1.125 1.00 1.00 PROA N
ATOM 212 CA PRO B 13 23.015 -14.591 -1.740 1.00 1.00 PROA C
ATOM 213 C PRO B 13 23.615 -15.966 -1.497 1.00 1.00 PROA C
ATOM 214 CB PRO B 13 23.871 -13.536 -1.058 1.00 1.00 PROA C
ATOM 215 CG PRO B 13 23.267 -13.395 0.296 1.00 1.00 PROA C
ATOM 216 CD PRO B 13 21.794 -13.589 0.088 1.00 1.00 PROA C
ATOM 217 OT1 PRO B 13 23.006 -16.748 -0.718 1.00 0.00 PROA O
ATOM 218 OT2 PRO B 13 24.693 -16.260 -2.081 1.00 0.00 PROA O
ATOM 219 HA PRO B 13 22.941 -14.484 -2.810 1.00 0.00 PROA H
ATOM 220 HB1 PRO B 13 23.832 -12.574 -1.612 1.00 0.00 PROA H
ATOM 221 HB2 PRO B 13 24.929 -13.868 -0.988 1.00 0.00 PROA H
ATOM 222 HG1 PRO B 13 23.671 -14.164 0.989 1.00 0.00 PROA H
ATOM 223 HG2 PRO B 13 23.475 -12.388 0.717 1.00 0.00 PROA H
ATOM 224 HD1 PRO B 13 21.330 -14.115 0.949 1.00 0.00 PROA H
ATOM 225 HD2 PRO B 13 21.280 -12.620 -0.086 1.00 0.00 PROA H
TER 226 PRO B 13
END

4

This is a messed up PDB file which has lost its proper column formatting.

Attach it a txt file for example.
Or preserve the proper formatting.
If this is the formatting in your PDB, then you have a problem.

5

Sorry for that, here it is as an attachment (didn’t have enough trust points before).

Glycan_reres_final.pdb (18.0 KB)

6

OK - found the issue - we are not supporting (yet) THR-glycosylation.

Already working on it and got it to work for your PDB!

Implement THR-glycosylation · Issue #1371 · haddocking/haddock3 · GitHub

So wait a bit - it will be available soon.

7

Amazing thanks so much, I’m looking forward to it :slight_smile:

8

Hi there

The THR-linkage is now implemented!

You will have to get the latest haddock3 version and install it.

Note that a pip install haddock3 will not have the update as we have not yet defined a new release.

So you will have to get the code directly and install it via pip install .

9

I actually grabbed your commit earlier and can confirm that it also works on my end :slight_smile:

I have to say, I am blown away by the responsiveness and helpfulness → Thank you!

10

:slight_smile::slight_smile:

11

Just realised when implementing it in haddock2.5 that some parameters were missing in case you would keep all hydrogens (delenp = true in topoaa module).

Fixed now :slight_smile:

1 Like