Hello,
As I understand the haddock 2.4 webserver now supports docking with glycoproteins. However, ¿is it possible to configure the local version (also 2.4) to also have said feature?
Thank you very much in advance
The local version also supports it out of the box, as long as you follow the supported nomenclature
See for the residue naming: HADDOCK Web Server - Settings
Hello prof. Bonvin,
Do I need to specify a special topology or make some modification in the run.cns file? Because I still get the following error in the generate_1.out file (molecule 1 is my glycoprotein): “residue NAG not found in topology files. Add topology definition.”
I think my nomenclature is OK. I am attaching the pdb file of the glycoprotein.
If you need another file or information let me know.
Thanks in advance
tlr4-clean.pdb (957.4 KB)
The support for glycoproteins was added in the July release of HADDOCK2.4
You can check in the test directory if you have the glycans test.
If not, then send me an email and I will send you the info to get the latest release.
Thank you professor. I have just checked and the glycan test is not there. I have just send you an email to get the latest update.
Gabriel
Hello Prof. Bonvin
I updated my PDB file and my glycoprotein nomenclature is also fine. But I still getting “XXX” in place of NAG and BMA glycosylation when I uploaded my PDB in HADDOC2.4 server. Please help me to resolve this issue.
Thank You
Do you mean in the display window for active/passive residues?
This is normal. We only name the amino acid and nucleic acids.