I am docking a charged ligand to a protein, in which charge interactions may play an important role. My ligand in this case is tetraphenylphosphonium (TPP+) cation, which may be strongly interacting with glutamate residues. I have converted GLU to GLH as necessary for deprotonated/protonated states to take care of the protein side. How do you specify charge for the ligand?
I would ideally model the TPP+ cation as having a +1 charge delocalized over different atoms in TPP, but at the very least, I would like the docking simulation to consider a +1 charge on the P atom of TPP.
I can specify the charge in the PDB file, but does HADDOCK read the charge column of PDB files?
You can not control the charge of the ligand on the server…
We use a version of PRODRG to generate ligand parameters and there is not control of the charge. You can only hope PRODRG will generate the correct charge state.
And HADDOCK does not read the charge column of PDB files.