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J Biomol NMR


Title:The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules
Author(s):Luginbuhl P; Guntert P; Billeter M; Wuthrich K;
Address:"Institut fur Molekularbiologie und Biophysik, Eidgenossische Technische Hochschule-Honggerberg, Zurich, Switzerland"
Journal Title:J Biomol NMR
Year:1996
Volume:8
Issue:2
Page Number:136 - 146
DOI: 10.1007/BF00211160
ISSN/ISBN:0925-2738 (Print) 0925-2738 (Linking)
Abstract:"A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints"
Keywords:"*Computer Simulation Glutaredoxins *Models, Molecular Models, Theoretical Movement *Oxidoreductases Proteins/*chemistry Protozoan Proteins/*chemistry *Software Water/chemistry;"
Notes:"MedlineLuginbuhl, P Guntert, P Billeter, M Wuthrich, K eng Comparative Study Research Support, Non-U.S. Gov't Netherlands 1996/09/01 J Biomol NMR. 1996 Sep; 8(2):136-46. doi: 10.1007/BF00211160"

 
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