PRODRG> Atom is bonded to multiple atoms

HADDOCK
1

I’m trying to dock the attached ligand with a DNA fragment. I’m getting this error which I don’t know how to handle. Removing CONNECT records or saving with PyMOL doesn’t fix it.

“The following error occurred when processing one of your PDB file: Unable to generate topology for ligand UNK. PRODRG did not create the required output: PRODRG> C1 is bonded to C7 N2 O2 C27 C28 C29 C31”

HETATM    1  C1  UNK     1      21.747  -9.787   0.000  1.00  0.00           C
HETATM    2  C2  UNK     1      19.149 -10.287   0.000  1.00  0.00           C
HETATM    3  C3  UNK     1      17.312 -11.281   0.000  1.00  0.00           C
HETATM    4  N1  UNK     1      12.769 -10.244   0.000  1.00  0.00           N
HETATM    5  C4  UNK     1      17.417 -10.287   0.000  1.00  0.00           C
HETATM    6  C5  UNK     1      13.438  -9.501   0.000  1.00  0.00           C
HETATM    7  C6  UNK     1      18.283  -9.787   0.000  1.00  0.00           C
HETATM    8  C7  UNK     1      20.881 -10.287   0.000  1.00  0.00           C
HETATM    9  S1  UNK     1      11.960  -8.843   0.000  1.00  0.00           S
HETATM   10  C8  UNK     1      14.433  -9.605   0.000  1.00  0.00           C
HETATM   11  C9  UNK     1      14.840 -10.519   0.000  1.00  0.00           C
HETATM   12  C10 UNK     1      15.834 -10.623   0.000  1.00  0.00           C
HETATM   13  N2  UNK     1      20.015  -9.787   0.000  1.00  0.00           N
HETATM   14  C11 UNK     1      12.938  -8.635   0.000  1.00  0.00           C
HETATM   15  N3  UNK     1      16.503  -9.880   0.000  1.00  0.00           N
HETATM   16  O1  UNK     1      18.283  -8.787   0.000  1.00  0.00           O
HETATM   17  O2  UNK     1      20.881 -11.287   0.000  1.00  0.00           O
HETATM   18  O3  UNK     1      15.021  -8.796   0.000  1.00  0.00           O
HETATM   19  O4  UNK     1      14.252 -11.328   0.000  1.00  0.00           O
HETATM   20  C12 UNK     1      11.856  -9.837   0.000  1.00  0.00           C
HETATM   21  S2  UNK     1      16.334 -11.489   0.000  1.00  0.00           S
HETATM   22  C13 UNK     1      10.990 -10.337   0.000  1.00  0.00           C
HETATM   23  N4  UNK     1      10.124  -9.837   0.000  1.00  0.00           N
HETATM   24  C14 UNK     1       9.258 -10.337   0.000  1.00  0.00           C
HETATM   25  C15 UNK     1       8.392  -9.837   0.000  1.00  0.00           C
HETATM   26  O5  UNK     1       9.258 -11.337   0.000  1.00  0.00           O
HETATM   27  C16 UNK     1       7.525 -10.337   0.000  1.00  0.00           C
HETATM   28  C17 UNK     1       7.421 -11.332   0.000  1.00  0.00           C
HETATM   29  C18 UNK     1       6.612  -9.931   0.000  1.00  0.00           C
HETATM   30  N5  UNK     1       6.443 -11.540   0.000  1.00  0.00           N
HETATM   31  C19 UNK     1       5.943 -10.674   0.000  1.00  0.00           C
HETATM   32  C20 UNK     1       8.399 -11.540   0.000  1.00  0.00           C
HETATM   33  C21 UNK     1       7.730 -12.283   0.000  1.00  0.00           C
HETATM   34  O6  UNK     1       4.948 -10.569   0.000  1.00  0.00           O
HETATM   35  C22 UNK     1       6.404  -8.952   0.000  1.00  0.00           C
HETATM   36  N6  UNK     1       5.490  -8.546   0.000  1.00  0.00           N
HETATM   37  C23 UNK     1       7.073  -8.209   0.000  1.00  0.00           C
HETATM   38  C24 UNK     1       5.595  -7.551   0.000  1.00  0.00           C
HETATM   39  C25 UNK     1       6.573  -7.343   0.000  1.00  0.00           C
HETATM   40  C26 UNK     1       4.852  -6.882   0.000  1.00  0.00           C
HETATM   41  C27 UNK     1      22.613 -10.287   0.000  1.00  0.00           C
HETATM   42  C28 UNK     1      22.718 -11.281   0.000  1.00  0.00           C
HETATM   43  C29 UNK     1      23.527  -9.880   0.000  1.00  0.00           C
HETATM   44  N7  UNK     1      23.696 -11.489   0.000  1.00  0.00           N
HETATM   45  C30 UNK     1      24.196 -10.623   0.000  1.00  0.00           C
HETATM   46  C31 UNK     1      21.739 -11.489   0.000  1.00  0.00           C
HETATM   47  C32 UNK     1      22.409 -12.232   0.000  1.00  0.00           C
HETATM   48  O7  UNK     1      25.190 -10.519   0.000  1.00  0.00           O
HETATM   49  C33 UNK     1      23.735  -8.902   0.000  1.00  0.00           C
HETATM   50  N8  UNK     1      24.648  -8.495   0.000  1.00  0.00           N
HETATM   51  C34 UNK     1      23.065  -8.159   0.000  1.00  0.00           C
HETATM   52  C35 UNK     1      24.544  -7.501   0.000  1.00  0.00           C
HETATM   53  C36 UNK     1      23.566  -7.293   0.000  1.00  0.00           C
HETATM   54  C37 UNK     1      25.287  -6.832   0.000  1.00  0.00           C
END
2

Try to visualize your ligand… You will see you have a problem…

Nothing we can do on our side.

3

Sorry to reply to this so late I’ve been trying other programs but would like to come back to HADDOCK. My ligand is Colibactin and when I visualized it in PyMOL, it looks fine. Here’s the SMILES string. What would be the best way of generating a structure that is compatible with HADDOCK? I tried to get a pdb from OpenBabel but still can’t make it work.

C[C@H]1CCC(=N1)C2=C(C3(CC3)NC2=O)CC(=O)NCC4=NC(=CS4)C(=O)C(=O)C5=NC(=CS5)C(=O)CNC(=O)CC6=C(C(=O)NC67CC7)C8=NC@HC

4

Did you visualise the file you pasted in a previous post?
This is how it looks in pymol on my side:

Screenshot 2024-07-19 at 15.37.10
Screenshot 2024-07-19 at 15.37.10844×315 104 KB

5

We do have a tutorial that describes the generation of ligand conformations from smile strings for HADDOCK using RDKIT. Check:

6

OK thank you very much I’ll see if I can make it work following the tutorial.