Hi Subhash,
I am working on a enzyme-ligand complex structure. For some analysis I need to
remove wander wall interactions between protein and ligand. How can I do that in
Phenix? Something similar to igroup statement in CNS?
A simple trick is to assign altloc characters to the ligand and the parts of the protein that shouldn't interact, e.g. set column 17 of the protein atom records to "A" and in all ligand records assign "B". There will be no van-der-Waals interactions between A and B, only between blank-X and X-X, where X is A or B. The situations where you'd use an igroup statement in CNS are handled more automatically in phenix, via inspection of altlocs and occupancies. I'm curious why you'd want to turn off the van-der-Waals interactions too the ligand. Without them it could bump into the protein, which isn't physically possible. Could you explain? Ralf