New Method for Direct Linear-Scaling Calculation of Electron Density of Proteins

A new scheme for direct linear-scaling quantum mechanical calculation of electron density of protein systems is developed. The new scheme gives much improved accuracy of electron density for proteins than the original MFCC (molecular fractionation with conjugate caps) approach in efficient linear-scaling calculation for protein systems. In this new approach, the error associated with each cut in the MFCC approach is estimated by computing the two neighboring amino acids in both cut and uncut calculations and is corrected. Numerical tests are performed on six oligopeptide taken from PDB (protein data bank), and the results show that the new scheme is efficient and accurate. Recently, a highly efficient approach for full quantum mechanical computation of electronic properties of polymers such as proteins has been developed.1-3 In this molecular fractionation with conjugate caps (MFCC) approach, a protein, for example, is decomposed into amino acid-based fragments and pairs of conjugate caps (concap) are inserted at the cuts to properly cap the fragments. By employing the MFCC approach, one can compute electronic properties of protein systems suc