GLYCANS problem

HADDOCK
1

Hello all,
I have the following problem.

I want to perform a protein-polysaccharides docking, so I did the following steps (also following the suggestion found in this topic: Bond missing for branched glycans (protein carbohydrate docking)):

  1. I generated PDB e PSF files from glycans server (http://haddock.science.uu.nl/enmr/services/GLYCANS/),
  2. Put the .pdb and .psf file in the run1/begin directory
  3. After several try, I also added a file_B.list file in the same directory along the line of the file_A.list file created by CNS.
  4. What I got after the generate_complex step is a merged PDB file where all the coordinates of the second molecule are as follow:

…
ATOM 1053 CA ASN 120 -45.902 12.133 -8.508 1.00 10.00 A
ATOM 1054 C ASN 120 -44.818 13.184 -8.764 1.00 10.00 A
ATOM 1055 O ASN 120 -44.273 13.189 -9.856 1.00 10.00 A
ATOM 1056 OXT ASN 120 -44.550 13.962 -7.864 1.00 10.00 A
ATOM 1057 C1 GCP 1 9999.0009999.0009999.000 1.00 10.00 GLYC
ATOM 1058 H1 GCP 1 9999.0009999.0009999.000 1.00 10.00 GLYC
ATOM 1059 C2 GCP 1 9999.0009999.0009999.000 1.00 10.00 GLYC
ATOM 1060 H2 GCP 1 9999.0009999.0009999.000 1.00 10.00 GLYC
ATOM 1061 O2 GCP 1 9999.0009999.0009999.000 1.00 10.00 GLYC
…

I am running HADDOCK locally.

Where is the problem?

Thanks in advance for your help.
Best,
Francesco

2

Make sure to remove first all chainIDs and segIDS

Does it work if you only provide a single structure ?

3

Thanks for your quick answer.

I removed all the chainIDs and the segIDs but unfortunately the problem still remains.

I am docking a single structure of a protein with a single structure of a polysaccharide.

4

At this point we would need the full archive of your run dir to help you further. Send it to our support email

5

OK. Will do.
Thanks
Francesco