The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.4
Hello, this is my first time to edit protein pdb file for Haddock. My problem is there is no pdb_format.py file in pdb_tools or Haddock_tools. I do find the file pdb_strict_format.py in the haddock-tools package. When I run pdb_strict_format.py mypdb file, but get the following error message:
Traceback (most recent call last):
File “pdb_strict_format.py”, line 235, in
f_pdb = PDBParser(args.pdb, args.no_chainid)
File “pdb_strict_format.py”, line 97, in init
self._parse(chain_id_check)
File “pdb_strict_format.py”, line 198, in _parse
atom = self._parse_atom_line(line, chain_id_check)
File “pdb_strict_format.py”, line 128, in _parse_atom_line
icode, x, y, z, o, b, segid) = atom_data.groups()
ValueError: need more than 13 values to unpack
Could you please tell me where I can find the pdb_format.py or how to use pdb_strict_format.py to get right format pdb file for haddock.
Thank you,
Handa
Hi! Could you please give us more detail on what you are trying to do? Also have a look at our tutorials, they cover all the steps from preparation to analysis: https://www.bonvinlab.org/education/HADDOCK24
good luck! 