Interested in building a bonded metal ion force field compatible with AMBER? MTK++ and MCPB are designed to facilitate this process. The only caveat is that you should test any model generated using these tools before using it extensively in MD simulations! The details of this software suite are contained in the first manuscript and examples of its use are given in the remaining publication. See the manuals for more details on using the software.
- Peters, M. B., Yang, Y., Wang, B., Fuesti-Molnar, L., Weaver, M. N., and Merz, K. M., Jr. (2010) Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF), Journal of Chemical Theory and Computation 6, 2935-2947.
- Yang, Y., Chakravorty, D. K., and Merz, K. M., Jr. (2010) Finding a Needle in the Haystack: Computational Modeling of Mg(2+) Binding in the Active Site of Protein Farnesyltransferase, Biochemistry 49, 9658-9666.
- Chakravorty, D. K., Wang, B., Ucisik, M. N., and Merz, K. M. (2011) Insight Into the Cation-π Interaction at the Metal Binding Site of CusF Journal of the American Chemical Society 133, 19330–19333.
- Chakravorty, D. K., Wang, B., Lee, C. W., Giedroc, D. P., and Merz, K. M. (2011) Simulations of Allosteric Motions in the Zinc Sensor CzrA Journal of the American Chemical Society xx, yyy-zzz