One way of reducing the computational cost of calculations on large systems is by fragmentation. This splits the system into fragments, which leads to straightforward parallelization and less demanding computations. The Fragment Molecular Orbital (FMO) method is a well-known fragmentation method. The Effective Fragment Molecular Orbital (EFMO) method is a new method that combines the fragmentation scheme of the FMO method with the interaction energies of the Effective Fragment Potential (EFP) method. The FMO method has the ability to fragment over covalent bonds, allowing large proteins to be fragmented and analyzed. The EFMO method has recently added this capacity, but it has not been studied as extensively as it has been in the FMO method. Both methods have energy decomposition analyses (EDAs), which can be used to analyze the interactions within a protein conformation. The computational cost and accuracy with respect to ab initio methods is compared for the EFMO method and the FMO method for the Trp-cage protein (PDB code: 1L2Y). Additionally, the EDAs from the two methods are compared.

Analyzing protein structure with the effective fragment molecular orbital method

248th National Meeting (2014)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.