Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Deriving Force Field Dihedral Angle Parameters That Account For Conformation-Dependent Solvation Effects

Dihedral angle parameters in force fields are often obtained with the help of quantum chemical calculations. These are usually performed in vacuum and it is assumed that the solvent model used in the molecular dynamics simulation (explicit or implicit) satisfactorily accounts for the major part of the solvation energy. However, there are certain nonspecific solvation effects that are not properly accounted for in this approach. They relate to conformation-dependent solute polarization and solvation of conformation-dependent charge distribution. On an example of the glycosidic torsion we show that the contribution resulting from these effects is substantial and provides important correction to the torsion potential. A parameterization procedure is suggested that incorporates the missing conformation-dependent solvation effects into the torsion parameters, based on the difference between the quantum-mechanical self-consistent reaction field and Poisson-Boltzmann continuum solvation models. The suggested approach avoids double counting of solvation effects and provides parameters that may be used in combination with any of the widely used non-polarizable discrete solvent models or with the continuum solvent models. Improvements are demonstrated for the latest AMBER RNA χOL3 parameters. The suggested procedure may help to provide consistently better parameters than the conventional in vacuo parameterization approach.

Petr Jurečka1
Marie Zgarbová1
F. Javier Luque2
Jiří Šponer1,3
and Michal Otyepka1,3

1Department of Physical Chemistry Palacky University Olomouc, 17 listopadu 12, Olomouc, 771 46 Czech Republic
2Department de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain
3Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, Brno, 612 65, Czech Republic

Ph: (420) 585 634 760
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E-mail: petr.jurecka@upol.cz