All-electron density functional calculation on insulin with quasi-canonical localized orbitals.
An all-electron density functional (DF) calculation on insulin was performed by the Gaussian-based DF program, ProteinDF. Quasi-canonical localized orbitals (QCLOs) were used to improve the initial guess for the self-consistent field (SCF) calculation. All calculations were carried out by parallel computing on eight processors of an Itanium2 cluster (SGI Altix3700) with a theoretical peak performance of 41.6 GFlops. It took 35 h for the whole calculation. Insulin is a protein hormone consisting of two peptide chains linked by three disulfide bonds. The numbers of residues, atoms, electrons, orbitals, and auxiliary functions are 51, 790, 3078, 4439, and 8060, respectively. An all-electron DF calculation on insulin was successfully carried out, starting from connected QCLOs. Regardless of a large molecule with complicated topology, the differences in the total energy and the Mulliken atomic charge between initial and converged wavefunctions were very small. The calculation proceeded smoothly without any trial and error, suggesting that this is a promising method to obtain SCF convergence on large molecules such as proteins.
Inaba
Toru
T
Mechanical Engineering Research Laboratory, Hitachi, Ltd., 832-2 Horiguchi Hitachinaka, Ibaraki 312-0034, Japan.
Tahara
Saisei
S
Nisikawa
Nobutaka
N
Kashiwagi
Hiroshi
H
Sato
Fumitoshi
F
D000465:Algorithms; D000595:Amino Acid Sequence; D007328:Insulin / Q000737:chemistry*; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D055672:Static Electricity; D013816:Thermodynamics
D007328:Insulin; D011506:Proteins