Error in PDB file on web server

HADDOCK
1

Hi,

I keep getting the same error when uploading my files to the web server. I was wondering what it meant?

Here’s the error:

Error in PDB file.
Issue when parsing the PDB file at line 1 .
ATOM/HETATM line does not meet the expected format

This is what my .pdb file looks like (this isn’t the whole thing, it’s quite large):

generated by PyMOL 2.4.0

data_epyc1_R64G64_and_R71G71
_entry.id epyc1_R64G64_and_R71G71

_cell.entry_id epyc1_R64G64_and_R71G71
_cell.length_a 60.585
_cell.length_b 60.585
_cell.length_c 60.585
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
_symmetry.entry_id epyc1_R64G64_and_R71G71
_symmetry.space_group_name_H-M ‘P 1’

loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_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
ATOM 1 N N . ASN . . 1 ? 22.960 31.110 32.100 1.00 0.00 0 . 1
ATOM 2 C CA . ASN . . 1 ? 23.760 32.320 31.890 1.00 0.00 0 . 1
ATOM 3 C C . ASN . . 1 ? 25.190 31.930 32.290 1.00 0.00 0 . 1
ATOM 4 O O . ASN . . 1 ? 25.580 30.900 31.750 1.00 0.00 0 . 1
ATOM 5 C CB . ASN . . 1 ? 23.100 33.510 32.610 1.00 0.00 0 . 1
ATOM 6 C CG . ASN . . 1 ? 21.710 33.800 32.010 1.00 0.00 0 . 1
ATOM 7 N ND2 . ASN . . 1 ? 21.390 35.040 31.770 1.00 0.00 0 . 1
ATOM 8 O OD1 . ASN . . 1 ? 20.920 32.910 31.740 1.00 0.00 0 . 1
ATOM 9 N N . TRP . . 2 ? 25.820 32.550 33.300 1.00 0.00 0 . 1
ATOM 10 C CA . TRP . . 2 ? 27.080 32.090 33.960 1.00 0.00 0 . 1
ATOM 11 C C . TRP . . 2 ? 27.870 30.910 33.360 1.00 0.00 0 . 1

Apologies if this seems obvious, I’m not well versed in these things.

Thank you!

2

This is not a PDB format, but rather mmCIF. When saving from pymol select PDB as format.

Note that the 2.4 server should accept mmCIF.

3

Okay, I have tried to upload both mmCIF and PDB saved from Pymol but both come back with the same error.

4

In which version of the server?

Can you share your PDB file?

5

I have been using HADDOCK 2.4 web server.

I’ve managed to get it working with the pdb’s after cleaning them up

The mmCIF’s definitely aren’t working for whatever reason though.

Thank you!

6

Good!

Always good practice to clean the PDBs removing any unnecessary “junk” :slight_smile: