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J Phys Chem B. 2012 Apr 19;116(15):4646-54. doi: 10.1021/jp212474p. Epub 2012 Apr 9.

Development and testing of PFFSol1.1, a new polarizable atomic force field for calculation of molecular interactions in implicit water environment.

Author information

1
Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.

Abstract

A detailed calculation of protein interactions with explicitly considered water molecules takes enormous time. If water is considered implicitly (as media rather than as molecules), calculations become faster. These calculations are less precise, unless one uses voluminous computations of solvent-accessible areas. Our goal is to obtain parameters for nonbonded atom-atom interactions in implicitly considered water without computation of solvent-accessible areas. Because the "in-vacuum" interactions of atoms are obtained from experimental structures of crystals and enthalpies of their sublimation, the "in-water" interactions must be corrected using solvation free energies obtained from Henry's constants. Thus, we obtained parameters for the in-water van der Waals, electrostatic, and polarized interactions for atoms typical of protein structures. Parameters of covalent interactions were taken from the ENCAD force field and partial charges of atoms from quantum-mechanical calculations. The sought parameters of the in-water nonbonded interactions were optimized to achieve the best description of crystal structures and their sublimation and solvation at the room temperature. With the optimized parameters, the correlation between the calculated and experimental cohesion of molecules in crystals is 98.3% in the in-vacuum case (the supplementary force field PFFSubl1.1) and 95.4% the in-water case (the sought force field PFFSol1.1).

PMID:
22439906
DOI:
10.1021/jp212474p
[Indexed for MEDLINE]

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