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We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented. 相似文献
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We present a quantum mechanical approach to study protein-ligand binding structure with application to a Adipocyte lipid-binding protein complexed with Propanoic Acid. The present approach employs a recently develop molecular fractionation with a conjugate caps (MFCC) method to compute protein-ligand interaction energy and performs energy optimization using the quasi-Newton method. The MFCC method enables us to compute fully quantum mechanical ab initio protein-ligand interaction energy and its gradients that are used in energy minimization. This quantum optimization approach is applied to study the Adipocyte lipid-binding protein complexed with Propanoic Acid system, a complex system consisting of a 2057-atom protein and a 10-atom ligand. The MFCC calculation is carried out at the Hartree-Fock level with a 3-21G basis set. The quantum optimized structure of this complex is in good agreement with the experimental crystal structure. The quantum energy calculation is implemented in a parallel program that dramatically speeds up the MFCC calculation for the protein-ligand system. Similarly good agreement between MFCC optimized structure and the experimental structure is also obtained for the streptavidin-biotin complex. Due to heavy computational cost, the quantum energy minimization is carried out in a six-dimensional space that corresponds to the rigid-body protein-ligand interaction. 相似文献
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Three-dimensional time-dependent quantum wave packet calculation for the O((1)D)+HBr reaction has been carried out using an accurate ab initio global potential energy surface [K. A. Peterson, J. Chem. Phys. 113, 4598 (2000)]. The calculations show that the initial state-selected reaction probabilities are dominated by resonance structures, and the lifetime of the resonance is generally in the subpicosecond time scale. The energy dependence of the reaction cross section is computed, which manifests still resonance structures, and is a decreasing function of the translational energy. The thermal rate constants are also computed, which are nearly independent on the temperature. The calculation results are discussed and compared to similar reaction with deep well. 相似文献
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Bai JZ Bardon O Blum I Breakstone A Burnett T Chen GP Chen HF Chen J Chen SJ Chen SM Chen Y Chen YB Chen YQ Cheng BS Cowan RF Cui HC Cui XZ Ding HL Du ZZ Dunwoodie W Fan XL Fang J Fero M Gao CS Gao ML Gao SQ Gao WX Gratton P Gu JH Gu SD Gu WX Gu YF Guo YN Han SW Han Y Harris FA Hatanaka M He J He KR He M Hitlin DG Hu GY Hu HB Hu T Hu XQ Huang DQ Huang YZ Izen JM Jia QP Jiang CH Jin Y Jones L Kang SH Kelsey MH Kim BK Lai YF Lan HB Lang PF Lankford A Li F Li J Li PQ Li Q Li RB 《Physical review D: Particles and fields》1995,52(7):3781-3784
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