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?
Dear Alexandre,
I need you help.
I am trying to perform a docking with two ligands.
i have some questions:
- Is it possible to dock both ligands simultaneusly?could you give me some quick instructions?
- On the other hand, I have already performed a first docking with one of the ligands, and then save the structure in pymol and reopen haddock to perform the second docking with the other ligand. However when i tried to upload this second docking it says that the ligand need to be heteroatom?how i could rename it?where i have to put this tag.
Thanks in advance!
Regards,
Clarisa
- Is it possible to dock both ligands simultaneusly?could you give me some quick instructions?
Yes - change the number of molecules to dock to 3.
- On the other hand, I have already performed a first docking with one of the ligands, and then save the structure in pymol and reopen haddock to perform the second docking with the other ligand. However when i tried to upload this second docking it says that the ligand need to be heteroatom?how i could rename it?where i have to put this tag.
The PDBs returned by HADDOCK indeed have the lines corresponding to ligands written as ATOM and not HETATM.
You can edit the PDB file and change back the “ATOM “ to “HETATM” (Note here that you should include two spaces after ATOM to ensure that you are not changing the column ordering).
ATOM 4501 C CG1 . ILE A . 491 ? -17.113 6.598 21.521 1.00 15.00 0 A 1
ATOM 4502 C CG2 . ILE A . 491 ? -18.302 8.116 23.131 1.00 15.00 0 A 1
ATOM 4503 C CD1 . ILE A . 491 ? -16.337 7.727 20.878 1.00 15.00 0 A 1
ATOM 4504 H HN . ILE A . 491 ? -20.200 5.238 20.883 1.00 15.00 0 A 1
ATOM 4505 C C01 . HETATM A . 492 ? 4.772 -5.129 -1.306 1.00 15.00 0 A 1
ATOM 4506 O O01 . HETATM A . 492 ? 2.684 -4.601 -0.254 1.00 15.00 0 A 1
ATOM 4507 C C02 . HETATM A . 492 ? 4.041 -4.514 -0.295 1.00 15.00 0 A 1
ATOM 4508 O O02 . HETATM A . 492 ? 2.136 -7.195 -2.707 1.00 15.00 0 A 1
ATOM 4509 C C03 . HETATM A . 492 ? 2.184 -5.738 -0.807 1.00 15.00 0 A 1
ATOM 4510 O O03 . HETATM A . 492 ? 6.881 -5.571 -2.348 1.00 15.00 0 A 1
ATOM 4511 C C04 . HETATM A . 492 ? 1.034 -6.310 -0.272 1.00 15.00 0 A 1
i could not manage. Which could be the problem?
you said that i have to add two spaces by hand in each line of the protein? in order to not have this column ordening?
It will be too time consuming 
is any other way to perform it?
for the ligand, replace “ATOM “ by “HETATM” - nothing else!
in all atoms of the protein?
ATOM 4500 C CA . ILE A . 491 ? -18.474 7.021 22.082 1.00 15.00 0 A 1
ATOM 4501 C CG1 . ILE A . 491 ? -17.113 6.598 21.521 1.00 15.00 0 A 1
ATOM 4502 C CG2 . ILE A . 491 ? -18.302 8.116 23.131 1.00 15.00 0 A 1
ATOM 4503 C CD1 . ILE A . 491 ? -16.337 7.727 20.878 1.00 15.00 0 A 1
ATOM 4504 H HN . ILE A . 491 ? -20.200 5.238 20.883 1.00 15.00 0 A 1
ATOM 4505 C C01 . HETATM A . 492 ? 4.772 -5.129 -1.306 1.00 15.00 0 A 1
ATOM 4506 O O01 . HETATM A . 492 ? 2.684 -4.601 -0.254 1.00 15.00 0 A 1
I have this
This is WRONG!
Work from the original PDB file and only replace “ATOM “ by “HETATM” for all ligand atoms
I.e. speaking about the first 6 characters of each ligand line
I performed it, however it said that the format is wrong.
Error in PDB file.
Issue when parsing the PDB file at line 4545 .
ATOM/HETATM line does not meet the expected format
ATOM 4502 CD1 ILE A 491 -27.083 -3.268 7.482 1.00 15.00 A C
ATOM 4503 C ILE A 491 -30.990 -0.712 9.413 1.00 15.00 A C
ATOM 4504 O ILE A 491 -32.051 -0.319 8.924 1.00 15.00 A O
HETATM 4505 O02 UNK B 1 3.353 5.811 -3.072 1.00 15.00 B O
Could you help me?
I have not being able to dock two simultaneous ligands by changing the number of ligands to 3 and raising the pds of the two ligands and proteins. On the other hand, haddock doubles the docking with two molecules of one of the ligands, what could be the error?thanks in advance.
ATOM/HETATM line does not meet the expected format
which could be the problem?
Dear Sir/MAdam,
My run failed. I uploaded this pdbs attached. Could you explain me which could be the error?
I first dock one structure with ligand Quer (output: cluster1_4_1) and then with UDPglc, which gave this error.
Thanks in advance!
I will be waiting your reply.
Regards,
Clarisa
elbow.udpglu_pdb.001.pdb (6.48 KB)
elbow.quer_pdb_001.pdb (4.32 KB)
cluster1_4_1_haddock_2.pdb (361 KB)
A few issues:
-
It is best to delete all hydrogens from your ligand before submission (also in the HADDOCK model you edited)
-
Make sure your two ligands have different residue names
Attached the edited two PDB files that work fine is a short test.
cluster1_4_1_haddock_2.pdb (360.1 KB)
elbow.udpglu_pdb.001.pdb (2.9 KB)