Force Field Independent Metal Parameters Using a Nonbonded Dummy Model
نویسندگان
چکیده
منابع مشابه
Force Field Independent Metal Parameters Using a Nonbonded Dummy Model
The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we a...
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Abatrac-A procedure is given by which parameters of nonbonded interactions in a molecular mechanics energy function can be optimized for maximum compatibility with eb inif& force fields and structures. The method is based on a previously derived transformation of ob initio valence parameters to the molecular mechanics formalism. Explicit analytical expressions for the derivatives of the molecul...
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Modeling metalloproteins often requires classical molecular dynamics (MD) simulations in order to capture their relevant motions, which in turn necessitates reliable descriptions of the metal centers involved. One of the most successful approaches to date is provided by the "cationic dummy model", where the positive charge of the metal ion is transferred toward dummy particles that are bonded t...
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Metal ions are both ubiquitous to and crucial in biology. In classical simulations, they are typically described as simple van der Waals spheres, making it difficult to provide reliable force field descriptions for them. An alternative is given by nonbonded dummy models, in which the central metal atom is surrounded by dummy particles that each carry a partial charge. While such dummy models al...
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ژورنال
عنوان ژورنال: The Journal of Physical Chemistry B
سال: 2014
ISSN: 1520-6106,1520-5207
DOI: 10.1021/jp501737x