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Software

Moving-Domain QM/MM (MODQ3M), partitions a large molecular system into a number of smaller molecular domains (typically one or two amino acid residues per partition) and iteratively and self-consistently performs a set of QM/MM calculations redefining the QM region in each iteration. Since each QM/MM calculation is performed within the so-called Electronic Embedding (EE) approach, the QM regions are polarized by the MM region. Therefore, a mapping of the electronic density of each domain into a distribution of monopoles (or multipoles in general) provides electronic response to the specific chemical environment of each domain. The self-consistent cycle converges in three cycles yielding a QM derived point charge distribution for a large molecular system such as a protein.

The implementation details of the method are found in following papers:

1.) Gascón, J. A.; Leung, S. S. F.; Batista, E. R.; Batista, V. S. Journal of Chemical Theory and Computation. 2006, 2, 175-186.

2.) Menikarachchi, L. C.; Gascón, J. A. Journal of Molecular Modeling. 2008, 14, 479-487.

Development of MODQ3M is partially supported by a grant from the National Science Fundation

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