Using the Amber force field in X-plor

Tom Simonson and Dave Case have collaborated to implement the Amber force field and generalized Born solvation model into Xplor-NIH. This is primarily useful for NMR structure calculations (and especially for those persons who are already familiar with Xplor or CNS). There are interesting similarities and differences between the way sander and Xplor-NIH handle NMR analyses, but the similarities are probably more striking than the differences.

For a discussion of the effects of using the Amber/GB force field (rather than the Engh-Huber-based targets) see B. Xia, V. Tsui, D.A. Case, H.J. Dyson, and P.E. Wright. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. J. Biomol. NMR 22, 317-331 (2002).