My question is about Modeller restraints. Have you ever used of special_restraints or add_rsr to add your own restraints?

Or to build conserved part of your target protein (such as ligand binding site or binding state of ligand)?Did Modeller build

a model without any violation of your restraints?

My target protein has a conserved ligand binding site.But even when I give it the restraints ,it doesn't work exactly.(e.g. I gave it distance restraints with mean=2.3 Å and std=0.03 Å and one of pair_atom were in 3.7 Å from each other)

Is it common?Even about conserved parts of structure?

Thanks

Maryam