Thread: [Apbs-users] comparison of implicit solvent and explicit solvent calculation (fwd)
Biomolecular electrostatics software
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From: Frank D. D. <fr...@wa...> - 2004-06-11 22:53:04
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Hi Dr. Baker, I just received a messsage from a former colleague (see below). He, myself, and members of my group are interested in this upcoming article. Do you know when it will be published or do you have an available manuscript. Thanks. -- Frank Ducheneaux Caltech Division of Chemistry m/c 127-72 Pasadena, CA 91125 (626)395-2689 ---------- Forwarded message ---------- Date: Fri, 4 Jun 2004 14:58:33 +0530 (IST) From: Prabal K. Maiti <ma...@ph...> To: Shiang-Tai Lin <st...@wa...>, Frank D. Ducheneaux <fr...@wa...> Cc: Prof. William A Goddard III <wa...@wa...> Subject: comparison of implicit solvent and explicit solvent calculation Shiang-Tai/Frank Following might be usefull for you. Bill wanted me to do this. But I didnt have time before leaving. You were trying to do similar things/ So it is worth looking at it more closely. Prabal -------------------------------------------------------------------- Wagoner J, Baker NA. Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models. Journal of Computational Chemistry, accepted. Continuum electrostatics methods have become increasingly popular due to their ability to provide approximate descriptions of solvation energies and forces without expensive sampling required by explicit solvent models. In particular, the Poisson-Boltzmann equation (PBE) provides electrostatic potentials, solvation energies, and forces by modeling the solvent as a featureless, dielectric material and the mobile ions as a continuous distribution of charge. Polar solvation forces and energies obtained from the PBE are often supplemented with simple solvent-accessible surface area (SASA) models of apolar solvation. Given the recent development of methods which enable the use of PBE and SASA forces in molecular dynamics (MD) simulations, it is important to determine the ability of these implicit solvent models to accurately reproduce the solvation forces of more detailed explicit solvent simulations. In this paper, we compare PBE and SASA solvation forces with explicit solvent forces for several snapshots from an MD trajectory of intestinal fatty acid binding protein. The results from this comparison show that current implementations of the PBE are capable of generating polar solvation forces that correlate well with explicit solvent forces but systematically overestimate the magnitude of the interaction. SASA-based apolar forces are also found to correlate well with explicit solvent forces when atom-dependent SASA coefficients are used. SASA-based apolar models also systematically differ from explicit solvent calculations; however, such models underestimate the solvation force. The good correlation of implicit solvent forces with more detailed explicit solvent models is encouraging and implies that the systematic errors identified in these models could be corrected by appropriate parameterization of the force fields. -- ------------------------------------------------------------------------ Prabal K Maiti Email:ma...@ph... Deparment of Physics pk...@ya... Indian Institute of Science Tel:091-80-2293-2865 (O) Bangalore, 560012 :091-80-2351-7862 (H) India http://physics.iisc.ernet.in/~maiti Fax:091-80-2360-2602 ------------------------------------------------------------------------ |