Hello, what is the correct format for pdb for HADDOCK. I created a DNA pdb file from 3D-Dart. Every time I try to combine protein and DNA I will receive an email that says "pdb file contains an unknown amino acid or nucleic acid base T, make sure to use three letter code for bases and amino acid. "Is there any way I could fix this problem?
In the Step 4 of 3D-DART, untitled “For HADDOCK users” you have the option to make the output file HADDOCK ready, just check this option to get a PDB file pre-formatted to be used with HADDOCK.
If you still want to edit your PDB by yourself, then you need to convert the residue name column of your PDB file from " T " to “THY”.