A Fragment Quantum Mechanical Method for Metalloproteins

• DOI: 10.1021/acs.jctc.8b00966
• Publication Date: 2019-01-09T02:39:01Z
• Authors: Mingyuan Xu; Xiao He; Tong Zhu; John Z. H. Zhang
• Keywords: Metalloprotein; Force Field; Linear scale; Fragment (logic); Energy minimization

An accurate energy calculation of metalloprotein is crucial importance and also a theoretical challenge. In this work, metal molecular fractionation with conjugate caps (metal-MFCC) approach developed for efficient linear-scaling quantum potential atomic forces metalloprotein. approach, the given protein calculated by linear combination energies neighboring residues, two-body interaction between non-neighboring residues that are spatially in close contact binding group. The each fragment embedded field point charges representing remaining environment. Numerical studies were carried out to check performance method, all show excellent agreement full system calculations at M06-2X/6-31G(d) level. By combining dynamic simulation, we performed an ab initio structural optimization zinc finger high efficiency. present metal-MFCC low prefactor trivially parallelizable. individual typically contains about 50 atoms, it thus possible be higher levels chemistry method. This method can routinely applied perform simulation metalloproteins any size.