The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab
I want to use Haddock 2.4 between my DNA and ligand But When I load the my dna and ligand, I am getting these error for my dna and ligand separately.
for my dna structures it gives Error in PDB file. Issue when parsing the PDB file at line 2 .
ATOM/HETATM line does not meet the expected format
for ligand structures Error in PDB file.
Issue when parsing the PDB file at line 3 .
X,Y,Z coordinates, occupancy, and temperature (b) factors must be decimal numbers.
so Could anybody help me ho w to fix these error for my pdb files ?
The PDB format is very strict. Make sure that your files follow it.
Possible read your structures (models) in PyMol and export them again in PDB format.
Or check our pdb-tools server and try to fix your models.
Is there are HADDOCK script that can fix most of the PDB related issues when we download it from PDB databank?
It all depends on what you want to do. Some issues (e.g. ions naming) have to be done manually.
Have a look at our PBD-tools: https://wenmr.science.uu.nl/pdbtools/
Our new (still beta) haddock3 version does have a haddock3-pp command to preprocess PBD files and fix some issues automatically. But not thoroughly tested though.