I have trouble uploading the first protein that is a tetrameric structure solved by crystallographic.
It says: Error in PDB file. Your PDB contains multiple chains with overlapping numbering: A84 - B84 Consider selecting a chain or splitting your PDB.I previusly used PDB tools to make format on this, as was sugested. Nevermind, the problem continue.
I could not use one monomer or chain because i did and it perform docking wrongly. Could anyone help me?
Thanks in advance!
In that case you tetramer must be single chain for HADDOCK with non-overlapping residue numbering.
You will have to shift the numbering of chains 2 to 4 to avoid overlap in numbering.
This can be done with PDB-tools (locally or using the server)
Thanks I managed to run it!
However, i am trying another now i am having problems with .cif file, it says it is not a mmcif file. Could you help me?
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 C C1 . MLT . . 0 ? 1.871 0.184 0.057 0.00 0.00 0 . 1
HETATM 2 O O1 . MLT . . 0 ? 2.637 -0.512 -0.565 0.00 0.00 0 . 1
HETATM 3 O O2 . MLT . . 0 ? 2.264 1.392 0.491 0.00 0.00 0 . 1
HETATM 4 C C2 . MLT . . 0 ? 0.473 -0.300 0.342 0.00 0.00 0 . 1
HETATM 5 O O3 . MLT . . 0 ? 0.331 -1.645 -0.121 0.00 0.00 0 . 1
HETATM 6 C C3 . MLT . . 0 ? -0.534 0.597 -0.381 0.00 0.00 0 . 1
HETATM 7 C C4 . MLT . . 0 ? -1.934 0.189 0.000 0.00 0.00 0 . 1
HETATM 8 O O4 . MLT . . 0 ? -2.108 -0.725 0.771 0.00 0.00 0 . 1
HETATM 9 O O5 . MLT . . 0 ? -2.987 0.841 -0.516 0.00 0.00 0 . 1
HETATM 10 H H2 . MLT . . 0 ? 0.287 -0.264 1.415 0.00 0.00 0 . 1
HETATM 11 H HO3 . MLT . . 0 ? 0.483 -1.752 -1.070 0.00 0.00 0 . 1
HETATM 12 H H31 . MLT . . 0 ? -0.367 1.635 -0.095 0.00 0.00 0 . 1
HETATM 13 H H32 . MLT . . 0 ? -0.406 0.492 -1.459 0.00 0.00 0 . 1
HETATM 14 H HO5 . MLT . . 0 ? -3.866 0.544 -0.242 0.00 0.00 0 . 1
HETATM 15 H H6 . MLT . . 0 ? 3.169 1.661 0.281 0.00 0.00 0 . 1
Can you try converting it to a PDB file instead, e.g. using our pdb-tools server?
And upload the converted PDB
i used the pipeline as default and uploaded in haddock 2.4 and says:
Error in PDB file. Unknown error: list index out of range
which pdb i have to use?