ANE5 Glycan in Haddock Script form?

HADDOCK
2

Hi,

I’ve never seen the abbreviation ANE5, are you sure it is a monosaccharide? what is its canonical name? You can always find the list of supported carbohydrates here HADDOCK Web Server - Settings

3

Fucosylated Lewis A. Its made up of fucose and N-acetylglucosamines. I am pretty sure this is not on Haddock so am trying to find what could be most similar to it that is on haddocks library.

4

If you do so, it will no more be a Fucosylated Lewis A.

What you should do instead, is to input it as a Ligand in .pdb format.
Then we will automatically generate topology and compute parameters on the fly, for molecules that are out of the HADDOCK library.
You should then be able to use it.

If you really need to generate specific restraints:

  • have a first trial run with low sampling
  • download the results
  • find the ligand pdb file, its topology and parameters
  • generate specific restraints using the chain and atom names present in the pdb file
  • re-submit with the provided file
5

But this strategy will not allow for covalently linked glycans unfortunately.

If you were to generate topologies/parameters for ANE5, we could possibly integrate those into the ones supported by HADDOCK (after some testing)