Instances of ligand NAG do not contain the same atoms

HADDOCK
1

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

1 Like
2

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.

3

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

4

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.

5

everytime th error i got is this -instances of ligand LIG do not contain the same atoms.
can anyone please help me with this ?
here is my error giving file
HETATM 1 C51 LIG B 1 -3.250 0.846 -0.318 1.00 0.00 C
HETATM 2 C52 LIG B 1 -4.378 0.571 0.459 1.00 0.00 C
HETATM 3 C53 LIG B 1 -4.378 -0.522 1.330 1.00 0.00 C
HETATM 4 C54 LIG B 1 -3.249 -1.341 1.422 1.00 0.00 C
HETATM 5 C55 LIG B 1 -2.120 -1.067 0.646 1.00 0.00 C
HETATM 6 C56 LIG B 1 -2.108 0.032 -0.227 1.00 0.00 C
HETATM 7 C57 LIG B 1 -0.880 0.300 -1.067 1.00 0.00 C
HETATM 8 C58 LIG B 1 0.356 0.602 -0.256 1.00 0.00 C
HETATM 9 N01 LIG B 1 -1.107 1.385 -2.013 1.00 0.00 N
HETATM 10 O01 LIG B 1 0.293 0.714 0.962 1.00 0.00 O
HETATM 11 C59 LIG B 1 3.864 1.433 -1.206 1.00 0.00 C
HETATM 12 C60 LIG B 1 3.693 -0.168 -0.143 1.00 0.00 C
HETATM 13 N02 LIG B 1 4.551 0.289 -1.029 1.00 0.00 N
HETATM 14 S01 LIG B 1 4.921 2.876 -1.214 1.00 0.00 S
HETATM 15 O02 LIG B 1 4.015 -0.810 0.846 1.00 0.00 O
HETATM 16 C61 LIG B 1 5.942 0.361 -0.963 1.00 0.00 C
HETATM 17 C62 LIG B 1 6.446 1.788 -1.083 1.00 0.00 C
HETATM 18 C63 LIG B 1 7.305 1.960 -2.341 1.00 0.00 C
HETATM 19 C64 LIG B 1 7.217 2.193 0.181 1.00 0.00 C
HETATM 20 C65 LIG B 1 2.760 1.058 -0.186 1.00 0.00 C
HETATM 21 N03 LIG B 1 1.542 0.752 -0.895 1.00 0.00 N
HETATM 22 C66 LIG B 1 6.786 -0.839 -0.761 1.00 0.00 C
HETATM 23 O03 LIG B 1 6.270 -1.941 -0.678 1.00 0.00 O
HETATM 24 H01 LIG B 1 8.214 1.325 -2.295 1.00 0.00 H
HETATM 25 H02 LIG B 1 7.625 3.019 -2.443 1.00 0.00 H
HETATM 26 H03 LIG B 1 6.722 1.682 -3.245 1.00 0.00 H
HETATM 27 H04 LIG B 1 7.526 3.258 0.117 1.00 0.00 H
HETATM 28 H05 LIG B 1 8.132 1.580 0.314 1.00 0.00 H
HETATM 29 H06 LIG B 1 6.575 2.069 1.080 1.00 0.00 H
HETATM 30 P01 LIG B 2 -2.553 -15.135 -6.456 1.00 0.00 P1+
HETATM 31 C67 LIG B 2 -3.571 -13.605 -6.546 1.00 0.00 C
HETATM 32 C68 LIG B 2 -3.542 -16.474 -5.664 1.00 0.00 C
HETATM 33 C69 LIG B 2 -0.995 -14.719 -5.565 1.00 0.00 C
HETATM 34 C70 LIG B 2 -2.095 -15.712 -8.137 1.00 0.00 C
HETATM 35 C71 LIG B 2 -1.306 -16.858 -8.280 1.00 0.00 C
HETATM 36 C72 LIG B 2 -4.855 -13.581 -5.990 1.00 0.00 C
HETATM 37 C73 LIG B 2 -2.529 -15.019 -9.272 1.00 0.00 C
HETATM 38 C74 LIG B 2 -3.053 -12.453 -7.149 1.00 0.00 C
HETATM 39 C75 LIG B 2 -5.619 -12.411 -6.039 1.00 0.00 C
HETATM 40 C76 LIG B 2 -0.950 -17.310 -9.554 1.00 0.00 C
HETATM 41 C77 LIG B 2 -5.100 -11.262 -6.642 1.00 0.00 C
HETATM 42 C78 LIG B 2 -3.817 -11.283 -7.198 1.00 0.00 C
HETATM 43 C79 LIG B 2 -2.173 -15.470 -10.546 1.00 0.00 C
HETATM 44 C80 LIG B 2 -1.383 -16.616 -10.687 1.00 0.00 C
HETATM 45 C81 LIG B 2 -0.150 -13.734 -6.090 1.00 0.00 C
HETATM 46 C82 LIG B 2 -0.645 -15.368 -4.377 1.00 0.00 C
HETATM 47 C83 LIG B 2 1.036 -13.400 -5.431 1.00 0.00 C
HETATM 48 C84 LIG B 2 0.541 -15.035 -3.716 1.00 0.00 C
HETATM 49 C85 LIG B 2 1.382 -14.051 -4.244 1.00 0.00 C
HETATM 50 C86 LIG B 2 -3.120 -17.079 -4.475 1.00 0.00 C
HETATM 51 C87 LIG B 2 -4.732 -16.894 -6.270 1.00 0.00 C
HETATM 52 C88 LIG B 2 -3.884 -18.095 -3.894 1.00 0.00 C
HETATM 53 C89 LIG B 2 -5.496 -17.910 -5.690 1.00 0.00 C
HETATM 54 C90 LIG B 2 -5.073 -18.511 -4.501 1.00 0.00 C
HETATM 55 O04 LIG B 1 8.126 -0.731 -0.692 1.00 0.00 O1-

6

You have two ligands with the same residue name but different atom compositions. You should give unique residue name to each.

7

Hi! I’m trying to dock a trisaccharide in a receptor. The trisaccharide is formed by three units of beta-D-glucose linked by two beta1-3 glycosidic bonds. I used as input file for the glycan a pdb file with the same residue name, same residue number and different atom names for the three units as suggested, but at the end of the run the program generated the topology of just one of the three glucosyl units. here is the pdb file i used for the docking. please help :face_with_spiral_eyes:

HETATM 1 C1 BGC F 1 -3.078 4.682 2.356 1.00 0.00
HETATM 2 C2 BGC F 1 -4.577 4.443 2.650 1.00 0.00
HETATM 3 C3 BGC F 1 -5.295 5.798 2.826 1.00 0.00
HETATM 4 C4 BGC F 1 -4.608 6.674 3.900 1.00 0.00
HETATM 5 C5 BGC F 1 -3.081 6.808 3.616 1.00 0.00
HETATM 6 C6 BGC F 1 -2.311 7.496 4.757 1.00 0.00
HETATM 7 O1 BGC F 1 -2.392 3.447 2.368 1.00 0.00
HETATM 8 O2 BGC F 1 -5.172 3.712 1.583 1.00 0.00
HETATM 9 O3 BGC F 1 -6.644 5.552 3.200 1.00 0.00
HETATM 10 O4 BGC F 1 -5.240 7.949 3.891 1.00 0.00
HETATM 11 O5 BGC F 1 -2.483 5.488 3.404 1.00 0.00
HETATM 12 O6 BGC F 1 -2.281 6.662 5.913 1.00 0.00
HETATM 13 H1 BGC F 1 -2.945 5.174 1.371 1.00 0.00
HETATM 14 H2 BGC F 1 -4.665 3.861 3.590 1.00 0.00
HETATM 15 H3 BGC F 1 -5.284 6.338 1.857 1.00 0.00
HETATM 16 H4 BGC F 1 -4.751 6.202 4.892 1.00 0.00
HETATM 17 H5 BGC F 1 -2.951 7.418 2.699 1.00 0.00
HETATM 18 H6 BGC F 1 -4.539 3.018 1.369 1.00 0.00
HETATM 19 H7 BGC F 1 -6.901 4.786 2.675 1.00 0.00
HETATM 20 H8 BGC F 1 -6.182 7.751 3.857 1.00 0.00
HETATM 21 H9 BGC F 1 -2.255 5.762 5.571 1.00 0.00
HETATM 22 H10 BGC F 1 -1.276 7.712 4.431 1.00 0.00
HETATM 23 H11 BGC F 1 -2.763 8.475 5.005 1.00 0.00
HETATM 24 C7 BGC F 1 -0.321 1.376 0.000 1.00 0.00
HETATM 25 C8 BGC F 1 -1.333 1.671 1.130 1.00 0.00
HETATM 26 C9 BGC F 1 -1.542 3.196 1.256 1.00 0.00
HETATM 27 C10 BGC F 1 -0.201 3.942 1.447 1.00 0.00
HETATM 28 C11 BGC F 1 0.821 3.541 0.340 1.00 0.00
HETATM 29 C12 BGC F 1 2.235 4.094 0.593 1.00 0.00
HETATM 30 O7 BGC F 1 0.000 0.000 0.000 1.00 0.00
HETATM 31 O8 BGC F 1 -2.575 1.032 0.850 1.00 0.00
HETATM 32 O9 BGC F 1 -0.471 5.339 1.407 1.00 0.00
HETATM 33 O10 BGC F 1 0.922 2.083 0.242 1.00 0.00
HETATM 34 O11 BGC F 1 2.825 3.458 1.725 1.00 0.00
HETATM 35 H12 BGC F 1 -0.739 1.662 -0.987 1.00 0.00
HETATM 36 H13 BGC F 1 -0.924 1.280 2.083 1.00 0.00
HETATM 37 H14 BGC F 1 -2.036 3.567 0.336 1.00 0.00
HETATM 38 H15 BGC F 1 0.218 3.679 2.438 1.00 0.00
HETATM 39 H16 BGC F 1 0.464 3.948 -0.627 1.00 0.00
HETATM 40 H17 BGC F 1 -2.340 0.150 0.542 1.00 0.00
HETATM 41 H18 BGC F 1 -1.251 5.450 1.962 1.00 0.00
HETATM 42 H19 BGC F 1 2.478 2.560 1.716 1.00 0.00
HETATM 43 H20 BGC F 1 2.868 3.922 -0.298 1.00 0.00
HETATM 44 H21 BGC F 1 2.210 5.191 0.742 1.00 0.00
HETATM 45 C13 BGC F 1 -0.224 -2.923 -2.363 1.00 0.00
HETATM 46 C14 BGC F 1 -0.256 -2.171 -1.014 1.00 0.00
HETATM 47 C15 BGC F 1 -0.075 -0.657 -1.258 1.00 0.00
HETATM 48 C16 BGC F 1 1.203 -0.360 -2.077 1.00 0.00
HETATM 49 C17 BGC F 1 1.239 -1.212 -3.382 1.00 0.00
HETATM 50 C18 BGC F 1 2.578 -1.112 -4.135 1.00 0.00
HETATM 51 O12 BGC F 1 -0.217 -4.317 -2.127 1.00 0.00
HETATM 52 O13 BGC F 1 -1.494 -2.411 -0.351 1.00 0.00
HETATM 53 O14 BGC F 1 1.214 1.031 -2.379 1.00 0.00
HETATM 54 O15 BGC F 1 1.003 -2.625 -3.076 1.00 0.00
HETATM 55 O16 BGC F 1 3.617 -1.744 -3.391 1.00 0.00
HETATM 56 H22 BGC F 1 -1.104 -2.655 -2.984 1.00 0.00
HETATM 57 H23 BGC F 1 0.577 -2.539 -0.383 1.00 0.00
HETATM 58 H24 BGC F 1 -0.956 -0.275 -1.811 1.00 0.00
HETATM 59 H25 BGC F 1 2.090 -0.607 -1.460 1.00 0.00
HETATM 60 H26 BGC F 1 0.440 -0.847 -4.057 1.00 0.00
HETATM 61 H27 BGC F 1 0.523 -4.624 -2.660 1.00 0.00
HETATM 62 H28 BGC F 1 -1.657 -3.354 -0.456 1.00 0.00
HETATM 63 H29 BGC F 1 0.975 1.459 -1.549 1.00 0.00
HETATM 64 H30 BGC F 1 3.189 -2.477 -2.936 1.00 0.00
HETATM 65 H31 BGC F 1 2.486 -1.596 -5.126 1.00 0.00
HETATM 66 H32 BGC F 1 2.840 -0.055 -4.335 1.00 0.00

8

In that case you should rather define each unit as a separate residue as BGC is supported by HADDOCK.
And the atom names should be identical between the three units

And they can be defined as ATOM instead of HETATM

9

I’ve tried it, but it results in three separated glucosyl units (no glycosidic bonds)

10

The 1-3 linkage should be supported (if this is what you have). Can you share the PDB file with us (the one with the two units)?

12

Hi!

the “G3G3G_-90130_-90130.pdb” file is a pdb file generated with POLYS and it is the incriminated one. The “BG3G.pdb” file is the sperimental structure of the disaccharide (beta1-3 diglucose) and it perfectly works. Thank you for your support.

G3G3G_-90130_-90130.pdb (4.25 KB)

BG3G.pdb (2.79 KB)

13

Issue solved then! :slight_smile:

1 Like
14

Hi! I’ve tried to dock a triglucose with two beta1-3 glycosidic bonds (G3G3G), a diglucose with a beta1-4 glyosidic bond (G4G) and a diglucose with a beta1-6 glycosidic bond (G6G) with the suggested conditions (separated residues and same atom names) and again it results in three or two glucosyl units without glycosidic bonds. Here is attached a screenshot of the trisaccharide structure at the end of the run

G3G3G
G3G3G1050×830 29 KB

15

There are so many different linkages possible… Please send us PDB files for those system so that we can check and implement (if possible) the missing linkages

16

PS: Note a beta glucose should be named BGC as residue name. The 1-3 and 1-4 linkages should already be supported, the 1-6 one not (but should be simple to add).
So please provide PDB files for those cases so that we can test things on our side