Dear Charles or John; We are trying to use RDCs for the first time in our structure calculations, and would appreciate any examples of how one goes about implementing them in simulated annealing calculations on globular proteins. We have only the raw data (deltas from bicelle alignments). In particular, it would be nice if we could simultaneously get Da and Dr as in JMR 131, 159-162 (1998) Clore et al. I have looked at some of the example files we got with XPLOR-NIH, but I still haven't made sense of them.
In an almost unrelated question, we have also made use of the knowledge-based potentials in previous calculations, but it was not clear to me what kind of values to use for the energy scaling constants with these potentials. Because we have metal clusters, we have trouble with the torsional dynamics, and we are using Cartesian dynamics based on the old Nilges sa.inp routines from XPLOR. As such, I thought that perhaps the scaling constants that are defaults may be too small. Any thoughts? Thanks, Tom Pochapsky Brandeis Univ.
