All atom force field

HADDOCK
1

Dear community,

I am trying to dock a protein and a ligand, but I would like to do an all-atom model for my molecules and use a proton-proton NOE restraints for the unambiguous restraints.

Is there a recommended force field to include all atoms for a receptor and small molecule?

I did try running with OPLS and unchecking the box to remove non-polar hydrogens, but HADDOCK is still deleting the hydrogens of the ligand.

2

The PRODRG version we are using for ligands only keeps polar hydrogens.

Nothing to be done about it on the server.

If you run a local version you can provide your own topology and parameter files for the ligand (but non trivial)

If you want to still use the server, simply define your NOE restraints to the heavy atoms of the ligand, adding a small correction to the distance.