Error message - inconsistency in your data

HADDOCK
1

Hi, I have a trouble with protein-protein interaction, I am always receiving email with Error message - inconsistency in your data type of:
Second pdb file contains multiple forms of the same residue. This is not supported in the current form - I looked at it but all atoms were unique… I tried to edit it.

Than I receive Error message:
The second PDB has no ATOM lines with the specified chain(s)

or Error message:
Second pdb file is incorrectly formatted. Please align the columns of your PDB properly.

I honestly don’t know how to correct the PDB file (I am editing it in PSPad).
There appears to be always mistake.

Downloaded PDB file:

image
image1920×1080 202 KB

Edited PDB file:

image
image1920×1080 202 KB

I honestly don’t know what to do with it.

Thanks a lot for any advise,
Best regards,
Mirka

2

Looking at your screenshots I’m assuming you are trying to use 1cll, check the output below with pdb-tools;

$ pdb_fetch 1cll > 1cll.pdb
$ cat 1cll.pdb | grep ATOM | pdb_selaltloc > 1cll_fixed.pdb
$ diff 1cll.pdb 1cll_fixed.pdb | grep ATOM
< ATOM    896  CG AASP A 118      32.107   2.291  -1.516  0.50 13.30           C
< ATOM    897  CG BASP A 118      31.758   0.438  -0.326  0.50 22.66           C
< ATOM    898  OD1AASP A 118      31.940   2.877  -0.421  0.50 16.97           O
< ATOM    899  OD1BASP A 118      30.962   0.421   0.650  0.50 22.97           O
< ATOM    900  OD2AASP A 118      32.863   2.737  -2.402  0.50 16.23           O
< ATOM    901  OD2BASP A 118      32.886  -0.103  -0.173  0.50 22.16           O
# ...
> ATOM    896  CG  ASP A 118      32.107   2.291  -1.516  0.50 13.30           C
> ATOM    898  OD1 ASP A 118      31.940   2.877  -0.421  0.50 16.97           O
> ATOM    900  OD2 ASP A 118      32.863   2.737  -2.402  0.50 16.23           O

So it seems like your residue 118 should be:

ATOM    891  N   ASP A 118      29.174  -0.150  -1.906  1.00 10.98           N
ATOM    892  CA  ASP A 118      29.839   1.168  -1.812  1.00 10.40           C
ATOM    893  C   ASP A 118      29.437   2.041  -3.014  1.00 13.14           C
ATOM    894  O   ASP A 118      29.249   3.263  -2.842  1.00 16.62           O
ATOM    895  CB  ASP A 118      31.348   1.000  -1.697  1.00 16.46           C
ATOM    896  CG  ASP A 118      32.107   2.291  -1.516  0.50 13.30           C
ATOM    898  OD1 ASP A 118      31.940   2.877  -0.421  0.50 16.97           O
ATOM    900  OD2 ASP A 118      32.863   2.737  -2.402  0.50 16.23           O

Could you try using the snippet above and see if you can make the submission?

3

If you look at the screenshot you sent, you will see instances of AASP and BASP for residue 118.

This is a case where several side-chains conformations are seen in the crystal structure. You need to select only one of those.
This can be done with our PDB-tools server using the pdb_selaltloc command.

https://bianca.science.uu.nl/pdbtools/manual#pdb_selaltloc