A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin

TitleA combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin
Publication TypeJournal Article
Year of Publication2011
AuthorsNagata T, Fedorov DG, Sawada T, Kitaura K, Gordon MS
Journal TitleJournal of Chemical Physics
Volume134
Pages034110
Date Published01/21
ISBN Number0021-9606
Accession NumberISI:000286472200013
Keywordsbasis sets, dynamics simulation, energy gradients, FORCE-FIELD, large systems, method fmo, model, protein, structure prediction, water
Abstract

The gradient for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFP), denoted by FMO/EFP, was developed and applied to polypeptides solvated in water. The structures of neutral and zwitterionic tetraglycine immersed in water layers of 2.0, 2.5, 3.0, 3.5, 4.0, and 4.5 angstrom are investigated by performing FMO/EFP geometry optimizations at the RHF/cc-pVDZ level of theory for the solutes. The geometries optimized with FMO-RHF/EFP are compared to those from the conventional RHF/EFP and are found to be in very close agreement. Using the optimized geometries, the stability of the hydrated zwitterionic and neutral structures is discussed structurally and in terms of energetics at the second-order Moller-Plesset theory (MP2)/cc-pVDZ level. To demonstrate the potential of the method for proteins, the geometry of hydrated chignolin (protein data bank ID: 1UAO) was optimized, and the importance of the inclusion of water was examined by comparing the solvated and gas phase structures of chignolin with the experimental NMR structure. (C) 2011 American Institute of Physics. [doi:10.1063/1.3517110]

URL<Go to ISI>://000286472200013http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000134000003034110000001&idtype=cvips&doi=10.1063/1.3517110&prog=normal
DOI10.1063/1.3517110
Alternate JournalJ Chem Phys