Molecular mechanics and dynamics of biomolecules using a solvent continuum model.
An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson-Boltzmann equation (polar contribution) and the solvent-accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1830-1842, 2001
Fogolari
F.
F
Dipartimento Scientifico e Tecnologico, Universita' di Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy.
Esposito
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G
Viglino
P.
P
Molinari
H.
H