Instances of ligand NAG do not contain the same atoms

Hi! I am trying to dock an hexasaccharide in a receptor. For doing that, I have extracted the ligand (DP6) from the PDB of this ligand forming a complex with another protein (4MB5). I am trying to dock it but I receive always the following message:

There was an inconsistency in your data
Error message
Instances of ligand NAG do not contain the same atoms

I have checked the PDB of the ligand and there are not atom duplicated neither occupancies different to 1.0

Could you give me some advise?
Thanks in advance,
Enea

We have been docking oligosaccharides in the past with the server for a CAPRI target.
You have to define the oligosaccharide as HETATM and as a single residue, which means each unit will have the same residue number and unique atom names.
This requires some editing / renaming but is doable.

I assume that you are meaning this, right? (this is the PDB I am using when I receive the error)

HETATM 1 C1 NAG A 1 11.106 20.117 70.782 1.00 26.30 C
HETATM 2 C2 NAG A 1 12.087 21.266 71.026 1.00 26.33 C
HETATM 3 C3 NAG A 1 11.392 22.636 70.853 1.00 25.95 C
HETATM 4 C4 NAG A 1 10.575 22.704 69.540 1.00 25.36 C
HETATM 5 C5 NAG A 1 9.679 21.460 69.436 1.00 25.96 C
HETATM 6 C6 NAG A 1 8.876 21.382 68.155 1.00 26.37 C
HETATM 7 C7 NAG A 1 13.944 21.060 72.552 1.00 27.12 C
HETATM 8 C8 NAG A 1 14.466 21.317 73.957 1.00 27.13 C
HETATM 9 N2 NAG A 1 12.631 21.154 72.368 1.00 26.71 N
HETATM 10 O1 NAG A 1 11.788 18.912 70.781 1.00 27.08 O
HETATM 11 O3 NAG A 1 12.377 23.660 70.858 1.00 25.73 O
HETATM 12 O4 NAG A 1 9.736 23.882 69.541 1.00 24.49 O
HETATM 13 O5 NAG A 1 10.482 20.267 69.507 1.00 26.51 O
HETATM 14 O6 NAG A 1 9.728 21.208 67.035 1.00 28.26 O
HETATM 15 O7 NAG A 1 14.732 20.782 71.644 1.00 27.22 O
HETATM 16 H1 NAG A 1 10.347 20.109 71.564 1.00 0.00 H
HETATM 17 H2 NAG A 1 12.903 21.191 70.307 1.00 0.00 H
HETATM 18 H3 NAG A 1 10.717 22.795 71.694 1.00 0.00 H
HETATM 19 H4 NAG A 1 11.254 22.739 68.688 1.00 0.00 H
HETATM 20 H5 NAG A 1 8.987 21.461 70.278 1.00 0.00 H
HETATM 21 H62 NAG A 1 8.189 20.538 68.215 1.00 0.00 H
HETATM 22 H63 NAG A 1 8.305 22.302 68.032 1.00 0.00 H
HETATM 23 HN2 NAG A 1 12.009 21.148 73.164 1.00 0.00 H
HETATM 24 HO3 NAG A 1 12.101 24.373 70.277 1.00 0.00 H
HETATM 25 HO6 NAG A 1 9.200 21.161 66.235 1.00 0.00 H
HETATM 26 H81 NAG A 1 15.550 21.208 73.968 1.00 0.00 H
HETATM 27 H82 NAG A 1 14.022 20.599 74.646 1.00 0.00 H
HETATM 28 H83 NAG A 1 14.199 22.328 74.264 1.00 0.00 H
HETATM 29 HO1 NAG A 1 11.170 18.194 70.628 1.00 0.00 H
HETATM 30 C1 NAG A 2 10.166 25.032 68.890 1.00 23.02 C
HETATM 31 C2 NAG A 2 8.938 25.908 68.597 1.00 22.51 C
HETATM 32 C3 NAG A 2 9.332 27.313 68.125 1.00 22.23 C
HETATM 33 C4 NAG A 2 10.408 27.953 69.011 1.00 21.59 C
HETATM 34 C5 NAG A 2 11.562 26.959 69.213 1.00 22.13 C
HETATM 35 C6 NAG A 2 12.638 27.459 70.158 1.00 22.80 C
HETATM 36 C7 NAG A 2 6.841 25.026 67.793 1.00 23.13 C
HETATM 37 C8 NAG A 2 6.088 24.266 66.714 1.00 24.05 C
HETATM 38 N2 NAG A 2 8.127 25.279 67.571 1.00 22.67 N
HETATM 39 O3 NAG A 2 8.180 28.144 68.119 1.00 21.84 O
HETATM 40 O4 NAG A 2 10.884 29.152 68.354 1.00 20.47 O
HETATM 41 O5 NAG A 2 11.065 25.725 69.772 1.00 21.75 O
HETATM 42 O6 NAG A 2 13.677 26.498 70.301 1.00 23.43 O
HETATM 43 O7 NAG A 2 6.255 25.378 68.814 1.00 23.61 O
HETATM 44 H1 NAG A 2 10.674 24.772 67.961 1.00 0.00 H
HETATM 45 H2 NAG A 2 8.345 25.997 69.507 1.00 0.00 H
HETATM 46 H3 NAG A 2 9.716 27.243 67.107 1.00 0.00 H
HETATM 47 H4 NAG A 2 9.977 28.213 69.978 1.00 0.00 H
HETATM 48 H5 NAG A 2 12.016 26.748 68.245 1.00 0.00 H
HETATM 49 H62 NAG A 2 13.059 28.383 69.762 1.00 0.00 H
HETATM 50 H63 NAG A 2 12.195 27.656 71.134 1.00 0.00 H
HETATM 51 HN2 NAG A 2 8.542 25.032 66.684 1.00 0.00 H
HETATM 52 HO3 NAG A 2 8.216 28.746 68.866 1.00 0.00 H
HETATM 53 H81 NAG A 2 5.052 24.128 67.022 1.00 0.00 H
HETATM 54 H82 NAG A 2 6.555 23.293 66.562 1.00 0.00 H
HETATM 55 H83 NAG A 2 6.118 24.832 65.783 1.00 0.00 H
HETATM 56 HO6 NAG A 2 14.345 26.835 70.902 1.00 0.00 H

Yes BUT if the two NAG are connected, they should have the same residue number and the second one needs to have different atom names
It has to be treated as one unit for the server to accept it.