Dear experts, Is there a way to change the scale / weight of a subset of my dihedral restraints in the middle of a calculation? Maybe in a way analogous to defining classes of NOEs that get different scales?
Background: I am calculating the structure of a protein-ligand complex with XPLOR- NIH version 2.16.0 on a Mac. I have modified Michael Nilges' sa.inp protocol to first fold the protein while holding the ligand's coordinates fixed, then roughly positioning the ligand on the protein by switching on intermolecular NOEs and running some steps of MINImize RIGId, and finally refining everything with some DYNAmics VERLet. Now I know something about the geometry of intermolecular H-bonds from measuring J-couplings, and I would like to force a guanine base and an arginine guanidinium group to stay in a plane, by introducing (improper) dihedral restraints. I do not want these restraints to be active in the first phase, when the protein folds -- they should only take effect once the protein is folded and the ligand has roughly taken its place. Thanks for any solutions or workarounds, Martin Allan
