PDB upload error HADDOCK2.4

HADDOCK
1

Hi – I received this message when I upload my pdb file:
Error in PDB file. Unknown error: string index out of range

The pdb was created by ChemBioDraw and Chem3D Pro, then opened and saved by Pymol. The file looks like this:

HETATM 1 N 1 -3.440 -0.748 3.540 0.00 0.00 N
HETATM 2 N 1 -6.280 1.276 1.814 0.00 0.00 N
HETATM 3 N 1 -3.375 4.072 6.280 0.00 0.00 N
HETATM 4 N 1 -0.058 -1.494 0.306 0.00 0.00 N
HETATM 5 N 1 -4.046 -2.617 0.839 0.00 0.00 N
HETATM 6 N 1 -4.121 -0.493 0.826 0.00 0.00 N
…
HETATM 42 C 1 -2.258 -0.330 3.791 0.00 0.00 C
HETATM 43 C 1 -1.556 -0.609 4.900 0.00 0.00 C
HETATM 44 C 1 -2.138 -1.373 5.829 0.00 0.00 C
HETATM 45 C 1 -3.382 -1.804 5.580 0.00 0.00 C
HETATM 46 C 1 -4.005 -1.475 4.428 0.00 0.00 C
HETATM 47 C 1 -5.267 -1.869 4.159 0.00 0.00 C
HETATM 48 C 1 -5.830 -1.195 3.142 0.00 0.00 C
…
HETATM 138 H 1 -1.677 0.257 3.057 0.00 0.00 H
HETATM 139 H 1 -0.530 -0.234 5.043 0.00 0.00 H
HETATM 140 H 1 -1.614 -1.632 6.763 0.00 0.00 H
HETATM 141 H 1 -3.854 -2.416 6.363 0.00 0.00 H
HETATM 142 H 1 -7.601 -0.953 1.937 0.00 0.00 H
…
CONECT 268 123
CONECT 269 38
CONECT 270 38
CONECT 271 39
CONECT 272 39
CONECT 273 40
CONECT 274 125
CONECT 275 125
CONECT 276 41
END

2

Please could anyone help me understand what went wrong?

3

Your atoms have similar names…. All names must be unique!

4

Thanks for your comments!
I paste a section of a protein PDB below, as a reference:
ATOM 1 N HIS A 3 59.884 14.395 8.814 1.00 94.62 N
ATOM 2 CA HIS A 3 61.018 15.129 9.449 1.00 94.29 C
ATOM 3 C HIS A 3 61.937 14.160 10.181 1.00 92.24 C

If I want to edit my pdb, perhaps I could add a # after the atom for a unique name? like the following?
HETATM 1 N 1 1 -3.440 -0.748 3.540 0.00 0.00 N
HETATM 2 N 2 1 -6.280 1.276 1.814 0.00 0.00 N
HETATM 3 N 3 1 -3.375 4.072 6.280 0.00 0.00 N

5

Don’t put spaces in the name, i.e. rather: N1, N2, …

And also do not change the column order! if you add a number then remove a space.

6

Thank you!!
I prepared a test.pdb which contains the following as suggested:
MODEL 1
HETATM 1 N1 1 -3.440 -0.748 3.540 0.00 0.00 N
HETATM 2 N2 1 -6.280 1.276 1.814 0.00 0.00 N
HETATM 3 N3 1 -3.375 4.072 6.280 0.00 0.00 N
HETATM 4 N4 1 -0.058 -1.494 0.306 0.00 0.00 N
HETATM 5 N5 1 -4.046 -2.617 0.839 0.00 0.00 N
HETATM 6 N6 1 -4.121 -0.493 0.826 0.00 0.00 N
HETATM 7 N7 1 -1.134 -3.071 -1.838 0.00 0.00 N
HETATM 8 N8 1 -6.435 -0.303 -4.369 0.00 0.00 N
HETATM 9 N9 1 -6.685 -1.003 -2.301 0.00 0.00 N
HETATM 10 N10 1 -5.692 -2.249 -3.885 0.00 0.00 N
HETATM 11 N11 1 -3.380 1.815 2.158 0.00 0.00 N
HETATM 12 N12 1 -4.027 3.729 1.535 0.00 0.00 N

Rasmol opened it fine. but the submission form still shows an error:
Error in PDB file. Unknown error: string index out of range

7

You probably messed up the column order…

The PDB format is very strict! Compare your original and edited files.

Possibly read it in PyMol for example and export it again as PDB formatted file. This might correct some issues.

8

I have gone thru most of the troubles but failed at a final place:
Error in PDB file.
Issue when parsing the PDB file at line 137 .
Your PDB contains an elemental ion IR without specified charge

in fact, I added a charge to the end of the line, according to PDB handbook:
HETATM 137 Ir IR 12 -4.676 0.378 2.507 0.00 0.00 IR1+

now this is really frustrated. I don’t know how to correct this error.
Can you please help. thnx…

9

You should format ions according to HADDOCK Requirements. See:

https://bianca.science.uu.nl/haddock2.4/library

Note that the forum is searchable and the ion problem has been answered many times.

Also if the ion is part of your ligand it won’t work since we can not generate topologies for such systems.

10

Thank you I will check these out

11

Dear amjjbonvin,
I seemed to have corrected the ion charge issue. But I still can not get through the submission stage, as the following message occurred. I wonder what next I could do.

An error has occurred, here are the details: Error reading ‘/home/enmr/csb_webserver/data/process/haddock24/3592820364/523efefad33d3b70a612dfcc385ce1f2eb2006c4/protein2.pdb’.

12

As I explained previously, if the ion is part of the ligand it will not work…

14

Only residue numbers