Ligand Formatting

HADDOCK
1

Hello, I have a question regarding my ligand. When I upload my ligand to HADDOCK, I get the following error:

Error in PDB file.
Issue when parsing the PDB file at line 2.
ATOM/HETATM line does not meet the expected format

The first two lines of my ligand are the following:

AUTHOR GENERATED BY OPEN BABEL 2.3.90
HETATM 1 CL1 UNL A -14.336 1.578 1.012 1.00 0.00 Cl

For your ease, I am also attaching the screenshot to show the whitespace:

resim
resim819×64 3.33 KB

I tried using PDB Tools, but I received the following error:

Error uploading structure(s)

I only need to use the Tidy function in the PDB Tools, but I cannot figure out what is going wrong here.

Thank you for your time.

2
  • To know if your file is properly formatted, you can refer to this online resource : https://cupnet.net/pdb-format/.
  • Also, make sure the file extension is the appropriate one: .pdb.
  • I just tried an example using OpenBabel online version 3.1.1, with a Chlorine atom, (SMILES to PDB, 3D coordinates, add hydrogen) and it was functional.

See one not-functional and functional example (from SMILES ClCCCCOc1ccccc1):

3

Hello,

I edited all my ligands according to the resource you have linked, and everything worked! I think I was using an old guide for that, or somehow counted the spaces wrong, etc.

Thank you so much for your time and effort!