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Public Library of Science, PLoS ONE, 7(7), p. e41117, 2012

DOI: 10.1371/journal.pone.0041117

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The effective fragment molecular orbital method for fragments connected by covalent bonds

Journal article published in 2012 by Casper Steinmann ORCID, Casper Steinmann Svendsen, Dmitri G. Fedorov, Jan Halborg Jensen
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 {Å} for RHF and MP2, respectively. ; Comment: Revised manuscript