Docking HeparinSulfate to proteins using GlycanDock

Hi all,

back in the days I have use Rosetta for protein de novo prediction, but never went really deep into it.

I now wanted to use the GlycanDock application to dock an heparin molecule to a protein. However, GlycanDock does end during preparation with this error message:

ERROR: Cannot compute center of mass of zero residues!
ERROR:: Exit from: src/core/pose/util.cc line: 1408
protocols.jd2.JobDistributor: [ ERROR ]

I guess this message means, my heparin sulfate is not recognised as a proper sugar...

I executed the program like this:

GlycanDock.linuxgccrelease -include_sugars -alternate_3_letter_codes pdb_sugar -auto_detect_glycan_connections -in:file:s BMPin9.pdb -in:file:native BMP7.pdb -nstruct 1 -ex1 -ex2 -ex3 -ex4 -ex1aro -ex2aro -carbohydrates:glycan_dock:prepack_only true -docking:partners A_X -out:pdb

Here is a middle part of my PDB file with the end of the protein, the CONECT and LINK section and the start for the oligosaccharide...

[...]
ATOM    997  CE1 HIS A1103       2.003  92.207   7.176  1.00  0.00           C
ATOM    998  C   HIS A1103       3.872  88.265   5.980  1.00  0.00           C
ATOM    999  O   HIS A1103       3.582  87.126   6.178  1.00  0.00           O
ENDMDL
CONECT  988  989  990  986
CONECT  989  988
CONECT  990  988  991  998
CONECT  991  990  992
CONECT  992  991  993  995
CONECT  993  992  994  997
CONECT  994  993
CONECT  995  992  996
CONECT  996  995  997
CONECT  997  993  996
CONECT  998  990  999
CONECT  999  998
MODEL        2
LINK        O4   SGN     1                C1   IDS     2     1555   1555  1.40
LINK        O4   IDS     2                C1   SGN     3     1555   1555  1.40
LINK        O5S  SGN     3                C6   IDS     4     1555   1555  1.18
LINK        O4   IDS     4                C1   SGN     5     1555   1555  1.40
LINK        O4   SGN     5                C1   IDS     6     1555   1555  1.40
LINK        O4   IDS     6                C1   SGN     7     1555   1555  1.40
LINK        O4   SGN     7                C1   IDS     8     1555   1555  1.40
LINK        O4   IDS     8                C1   SGN     9     1555   1555  1.40
LINK        O4   SGN     9                C1   IDS    10     1555   1555  1.40
LINK        O4   IDS    10                C1   SGN    11     1555   1555  1.40
LINK        O4   SGN    11                C1   IDS    12     1555   1555  1.40
LINK        O4   IDS    12                C1   SGN    13     1555   1555  1.40
LINK        O4   SGN    13                C1   IDS    14     1555   1555  1.40
LINK        O4   IDS    14                C1   SGN    15     1555   1555  1.40
LINK        O4   SGN    15                C1   IDS    16     1555   1555  1.40
LINK        O4   IDS    16                C1   SGN    17     1555   1555  1.40
LINK        O4   SGN    17                C1   IDS    18     1555   1555  1.40
LINK        O4   IDS    18                C1   SGN    19     1555   1555  1.40
LINK        O4   SGN    19                C1   IDS    20     1555   1555  1.40
LINK        O4   IDS    20                C1   SGN    21     1555   1555  1.40
LINK        O4   SGN    21                C1   IDS    22     1555   1555  1.40
LINK        O4   IDS    22                C1   SGN    23     1555   1555  1.40
LINK        O4   SGN    23                C1   IDS    24     1555   1555  1.40
HETATM    1  C1  SGN X   1      49.602 116.355  18.526  1.00  0.00           C
HETATM    2  C2  SGN X   1      49.000 117.259  17.438  1.00  0.00           C
HETATM    3  C3  SGN X   1      48.324 118.475  18.084  1.00  0.00           C
HETATM    4  C4  SGN X   1      47.306 118.001  19.134  1.00  0.00           C
HETATM    5  C5  SGN X   1      48.026 117.077  20.132  1.00  0.00           C
HETATM    6  C6  SGN X   1      47.124 116.472  21.218  1.00  0.00           C
HETATM    7  N2  SGN X   1      50.049 117.664  16.503  1.00  0.00           N
HETATM    8  O1  SGN X   1      50.667 117.004  19.168  1.00  0.00           O
HETATM    9  O3  SGN X   1      47.629 119.202  17.092  1.00  0.00           O
HETATM   10  O4  SGN X   1      46.825 119.158  19.801  1.00  0.00           O
HETATM   11  O5  SGN X   1      48.617 115.986  19.445  1.00  0.00           O
HETATM   12  O6  SGN X   1      46.639 115.228  20.758  1.00  0.00           O
HETATM   13  S1  SGN X   1      50.758 116.524  15.571  1.00  0.00           S
HETATM   14  O1S SGN X   1      50.784 115.297  16.311  1.00  0.00           O
HETATM   15  O2S SGN X   1      49.978 116.447  14.370  1.00  0.00           O
HETATM   16  O3S SGN X   1      52.082 117.023  15.330  1.00  0.00           O
HETATM   17  S2  SGN X   1      45.675 114.254  21.508  1.00  0.00           S
HETATM   18  O4S SGN X   1      45.022 115.005  22.537  1.00  0.00           O
HETATM   19  O5S SGN X   1      44.760 113.814  20.491  1.00  0.00           O
HETATM   20  O6S SGN X   1      46.493 113.190  22.013  1.00  0.00           O
HETATM   21  C1  IDS X   2      45.450 119.225  20.043  1.00  0.00           C
HETATM   22  C2  IDS X   2      45.087 120.701  20.281  1.00  0.00           C
HETATM   23  C3  IDS X   2      43.618 120.955  19.935  1.00  0.00           C
HETATM   24  C4  IDS X   2      43.325 120.554  18.480  1.00  0.00           C
HETATM   25  C5  IDS X   2      44.378 119.547  17.978  1.00  0.00           C
HETATM   26  C6  IDS X   2      43.960 118.790  16.721  1.00  0.00           C
HETATM   27  O2  IDS X   2      45.280 120.993  21.653  1.00  0.00           O
[...]

Any tips? If it is the unknown glcan residue, how can I teach IDS and SGN to Rosetta? Or is there an easy way to rebuild this chain to a "rosetta standard"?

Thanks

Jan

PS: I attache the output if that helps...