Error in uploading the PDB file of ligand

[Yvette68]

Hi,

I am getting the following error when uploading my ligand file:
Error in PDB file. Unknown error: string index out of range
Attached are several lines in my pdb file. Could you please tell me how to fix it? Thank you very much!

HETATM 1 C 1 4.551 14.837 2.758 0.00 0.00 C
HETATM 2 C 1 5.605 13.836 3.219 0.00 0.00 C
HETATM 3 C 1 4.946 12.629 3.878 0.00 0.00 C
HETATM 4 C 1 3.849 12.060 2.987 0.00 0.00 C
HETATM 5 C 1 3.477 14.146 1.929 0.00 0.00 C

[amjjbonvin]

Several issues with that file:

1. It does not follow the correct PDB format

2. Each atom must have a unique atom name

[VGPReys]

Dear Yvette68,

• Probably you want to check this resource to make sure your formatting follows the standards: PDB format - Plouf
• Each atom must have a unique name
• Checkout our tutorials at: HADDOCK2.4 small molecule binding site screening – Bonvin Lab and HADDOCK2.4 shape-restrained protein-small molecule tutorial – Bonvin Lab

Cheers

[amjjbonvin]

Correction: for ligands it should remain HETATM

But the formatting of the file is important. It is not a space-separated format!

[Yvette68]

Problem solved, thank you!

[VGPReys]

Great to know !