Error in PDB file

HADDOCK
1

Error occurred on refinement page:
‘ATOM/HETATM line does not meet the expected format’
Please help me. What is wrong with my pdb.

ATOM 1 N LYS 1 64.944 45.432 22.846 1.00 0.00 N
ATOM 2 CA LYS 1 65.025 45.432 24.324 1.00 0.00 C
ATOM 3 C LYS 1 63.686 44.932 24.800 1.00 0.00 C
ATOM 4 O LYS 1 62.700 45.442 24.390 1.00 0.00 O
ATOM 5 CB LYS 1 65.376 46.772 24.981 1.00 0.00 C
ATOM 6 CG LYS 1 65.557 46.572 26.416 1.00 0.00 C
ATOM 7 CD LYS 1 66.091 47.862 26.989 1.00 0.00 C
ATOM 8 CE LYS 1 66.178 47.842 28.485 1.00 0.00 C
ATOM 9 NZ LYS 1 67.085 46.852 29.079 1.00 0.00 N1+
ATOM 10 H01 LYS 1 65.861 44.798 24.621 1.00 0.00 H
ATOM 11 H02 LYS 1 64.569 47.485 24.810 1.00 0.00 H
ATOM 12 H03 LYS 1 66.297 47.161 24.548 1.00 0.00 H
ATOM 13 H04 LYS 1 66.250 45.752 26.605 1.00 0.00 H
ATOM 14 H05 LYS 1 64.603 46.324 26.881 1.00 0.00 H
…
HETATM 1966 N1 LIP 130 47.880 66.597 40.050 0.00 0.00 N
HETATM 1967 N2 LIP 130 42.769 61.918 37.765 0.00 0.00 N
HETATM 1968 C1 LIP 130 39.381 65.383 34.588 0.00 0.00 C
HETATM 1969 C2 LIP 130 40.361 64.241 35.055 0.00 0.00 C
HETATM 1970 C3 LIP 130 42.274 64.059 36.562 0.00 0.00 C
HETATM 1971 C4 LIP 130 39.623 62.990 35.717 0.00 0.00 C
HETATM 1972 C5 LIP 130 40.737 61.985 36.268 0.00 0.00 C
HETATM 1973 C6 LIP 130 41.683 62.761 37.274 0.00 0.00 C
HETATM 1974 C7 LIP 130 42.645 66.264 37.593 0.00 0.00 C
HETATM 1975 C8 LIP 130 43.904 66.947 38.261 0.00 0.00 C
HETATM 1976 C9 LIP 130 45.152 67.069 37.289 0.00 0.00 C
HETATM 1977 C10 LIP 130 46.492 67.428 38.074 0.00 0.00 C
…
HETATM 2310 H98 LIP 130 45.273 61.571 39.009 0.00 0.00 H
HETATM 2311 1H99 LIP 130 44.355 48.998 49.540 0.00 0.00 H
HETATM 2312 H99 LIP 130 44.363 60.010 38.707 0.00 0.00 H
HETATM 2313 H100 LIP 130 40.298 67.112 34.739 0.00 0.00 H
HETATM 2314 H102 LIP 130 44.581 68.796 36.517 0.00 0.00 H
HETATM 2315 H103 LIP 130 52.089 66.192 35.243 0.00 0.00 H
HETATM 2316 H104 LIP 130 48.421 67.406 39.811 0.00 0.00 H
HETATM 2317 H105 LIP 130 43.313 61.462 37.056 0.00 0.00 H
CONECT 1966 1978 1994 2316
CONECT 1967 1973 2024 2317
CONECT 1968 1969 2080 2112 2142
CONECT 1969 1968 1971 2081 2115
CONECT 1970 1973 2081 2082 2118
…

2

Tye PDB format is very strict, don’t mess up the columns!

Compare the column order / positions to a file downloaded from the PDB.

3

Thanks a lot. I understood you and repaired columns.
Unfortunately, error occurred again.
This time:
‘Your PDB contains multiple forms of the same residue LIP 130 . This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble.’

But when I have seen this PDB through the visualizer softwares (pymol, vmd), everythings seems like in place.?

4

Rather edit the pdb text file and control you ligand - all atom names must be unique

5

Ok.
In the pdb text, ATOMs and HETATMs are separated by a TER. Can the atomic names in them be the same?
For example, if one of the ATOM lines contains an atom named C01, can an atom named C01 also exist in HETATM?

6

In the pdb text, ATOMs and HETATMs are separated by a TER. Can the atomic names in them be the same?

Yes provided the residue numbers are unique, i.e. not overlapping