Anywhere can generate a proper ligand PDB file? ChemDraw file is not working, and rewrite with pymol also not working

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

Anywhere can generate a proper ligand PDB file? ChemDraw file is not working, and rewrite with pymol also not working

2

You could use RDKit for this. You can generate ligand conformations from SMILE strings directly.

Some examples given in the following tutorial:

[

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HADDOCK2.4 shape-restrained protein-small molecule tutorial
bonvinlab.org
](https://www.bonvinlab.org/education/HADDOCK24/shape-small-molecule)
3

Thank you, but I don’t have a linux workstation available. Can you recommend any windows based software to do it? Many thanks.

4

You can install RDKit as python package.

You can also use OpenBabel online version (OPENBABEL - Chemical file format converter). For this, please set the following parameters:

  • Output format: PDB - Protein Data Bank format
  • Generate coordinates: 3D
  • Add / Delete hydrogens: Add