Bond missing for branched glycans (protein carbohydrate docking)

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2

Hello All,
In order to put the STD effects as an AIR restraints on the glycans, we treat the units that compose the glycans separated. For the linear glycans, it works well following the procedures:

1 . generate PDB files from glycans server. (http://haddock.science.uu.nl/enmr/services/GLYCANS/),
2. put carbohydrate.param, carbohydrate.top and .link file into the run1/toppar.
3. Run the haddock locally.

However, once I want to dock the hexa-saccharide Fuc(a1-2)Gal(b1-3)[Fuc(a1-4)]GlcNAc(b1-3)Gal(b1-4)Glc, which has a branched Fuc (residue number 4) on GlcNAc, problems happens.

The bond (1RP3) between GlcNAc (residue number 3) and Gal (residue 5) is missing from the PDB generated by GLYCANS server. Then I use Chimera to add the bond, but once running Haddock, the bond misses again and the GAL(residue 5)-GLC(residue 6) did not move with other parts of glycans during the docking as seen from the results. It seems that the glycan pdb generated in the begin directory also miss that bond.

I can provide files for each step if someone is interested in solving this problem.

Thanks,

Shen

2

Do you directly use in HADDOCK the psf file generated by GLYCANS? I.e. manually copying it into the begin dir making sure the naming is consistent with what is defined in run.cns?

And same thing for the corresponding PDB file

You can also check the psf file (look up the atoms forming the 1RP3 bond, note their number and then search in the list of bonds lower in the the psf file if that bond is defined or not.