Ligand submission problem/covalent docking

HADDOCK
1

Hello everyone,

I’m attempting to dock a covalent molecule, using HADDOCK 2.4 (done this before with different ligands). However, in this case, it appears that the ligand file cannot be submitted for some reason.

I’ve submitted the original PDB file, generated by Obabel, to both pdb_uniquename and pdb_tidy, followed by pdb_validate and everything seems ok, but I get the following error:

Error in PDB file.
Could not parse the PDB file at line 0: record unknown (COMPN)

I’ve also looked at my previous ligand submissions in terms of file structure, and they also contain these lines and worked with no issues.

Also tried to remove the first line(s) and just leave the HETATM records, but then get:

Error in PDB file.
Could not parse the PDB file at line 0: record unknown (HETAT)

Below is a part of the file, so that one can get an impression of the overall structure:

COMPND    UNNAMED                                                              
AUTHOR    GENERATED BY OPEN BABEL 2.3.2    
HETATM    1  C1  LIG     1      -1.706   8.945  -5.791  1.00  0.00           C  
HETATM    2  N1  LIG     1      -0.591   8.318  -5.071  1.00  0.00           N  
HETATM    3  C2  LIG     1      -0.900   8.258  -3.639  1.00  0.00           C  
HETATM    4  C3  LIG     1       0.235   7.727  -2.813  1.00  0.00           C  
HETATM    5  C4  LIG     1       0.142   6.581  -2.123  1.00  0.00           C  
HETATM    6  C5  LIG     1       1.218   6.133  -1.206  1.00  0.00           C  
HETATM    7  N2  LIG     1       1.157   4.829  -0.803  1.00  0.00           N  
HETATM    8  C6  LIG     1       0.596   3.715  -1.449  1.00  0.00           C  
HETATM    9  C7  LIG     1      -0.020   2.707  -0.704  1.00  0.00           C  
HETATM   10  O1  LIG     1      -0.336   2.739   0.629  1.00  0.00           O  
HETATM   11  C8  LIG     1      -0.726   3.990   1.187  1.00  0.00           C  
HETATM   12  C9  LIG     1      -0.325   1.492  -1.324  1.00  0.00           C  
HETATM   13  C10 LIG     1       0.014   1.223  -2.640  1.00  0.00           C  
HETATM   14  N3  LIG     1      -0.211  -0.009  -3.098  1.00  0.00           N  
HETATM   15  C11 LIG     1       0.182  -0.267  -4.346  1.00  0.00           C  
HETATM   16  N4  LIG     1       0.741   0.611  -5.179  1.00  0.00           N  
HETATM   17  C12 LIG     1       0.927   1.868  -4.728  1.00  0.00           C  
HETATM   18  N5  LIG     1       1.484   2.821  -5.632  1.00  0.00           N  
HETATM   19  C13 LIG     1       1.556   2.594  -7.031  1.00  0.00           C  
HETATM   20  C14 LIG     1       0.442   2.101  -7.735  1.00  0.00           C  
HETATM   21  C15 LIG     1       0.536   1.664  -9.071  1.00  0.00           C  
HETATM   22  S1  LIG     1      -0.843   0.696  -9.666  1.00  0.00           S  
HETATM   23  O2  LIG     1      -1.417   0.086  -8.490  1.00  0.00           O  
HETATM   24  N6  LIG     1      -2.061   1.773 -10.335  1.00  0.00           N  
HETATM   25  C16 LIG     1      -1.547   2.841 -11.298  1.00  0.00           C  
HETATM   26  C17 LIG     1      -0.961   2.271 -12.586  1.00  0.00           C

Any help would be appreciated,

Many thanks,

S

2

Try loading it into e.g. pymol and saving it again as a PDF formatted file.

May-be something weird with the format or the file encoding…

Did you defined it correctly as ligand when submitting it?

3

Dear Professor Bonvin,

On spot advice as always - it work by saving again via Pymol. Yes, it was originally submited as Ligand.

Thank you!