I am using Haddock 2.4 to check docking parameters between DNA and ligand . My DNA file contain Na ion and I format it as given in Haddock library but it still gives the error -
"Error in PDB file.Issue when parsing the PDB file at line 308.ATOM/HETATM line does not meet the expected format"
format of ions in my pdb file-
HETATM 307 NA+1 NA1D 101 8.118 -6.766 34.223 0.50 15.72 NA
HETATM 308 NA+1 NA1D 101 8.498 -6.164 34.656 0.50 20.12 NA
I have attached my pdb file of DNA
Sedighe Shokraei
Probably the problem with your PDB is that the residue order or the numbering of atoms is not correct. Use yasara software to renumbering
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