METHODS AND APPLICATIONS OF HYBRID QC/MM SIMULATIONS TO BIOMOLECULAR SYSTEMS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The workshop will present computational approaches for the simulation of enzymatic reactions. Lectures will be held on the relevant theoretical background including the applicability of Quantum Chemical (QC) methods for large molecules, re-parameterization of Semiempirical Molecular Orbital (SMO) methods for specific reactions, molecular mechanics (MM) force fields, hybrid QC/MM potential energy functions and simulation techniques on high performance computers. In-depth tutorials will be presented primarily with the use of the freely available pDynamo package developed in the lab of Dr. Martin J. Field and will also include developing SMO parameters for quantitatively accurate enzyme reaction simulations, the issues involved in constructing a QC/MM model and the various methods for generating energy profiles of bio-molecular reactions to determine mechanisms and structure-function relationships. Experience with pDynamo is helpful but not a prerequisite for attendance. The workshop is designed for graduate students, post-doctoral researchers and faculty in computational biophysics and physical organic chemistry who have experience with computational chemistry methods and seek to enhance their capabilities to include the modeling of enzymatic reactions. Participants are encouraged to discuss and work on bio-molecular systems from their own research during the workshop. Space is limited. This workshop is supported by the NIH-National Center for Research Resources.