Solvated ensemble averaging in the calculation of partial atomic charges.

ABSTRACT: In the calculation of partial atomic charges, for use in molecular mechanics or dynamics simulations, it is common practice to select only a single conformation for the molecule of interest. For molecules that contain rotatable bonds, it is preferable to compute the charges from several relevant conformations. We present here results from a charge derivation protocol that determines the partial charges by averaging charges computed for conformations selected from explicitly solvated MD simulations, performed under periodic boundary conditions. This approach leads to partial charges that are weighted by a realistic population of conformations and that are suitable for condensed phase simulations. This protocol can, in principle, be applied to any class of molecule and to nonaqueous solvatio

SUBMITTER: Basma M 

PROVIDER: S-EPMC1986576 | biostudies-literature | 2001 Aug

REPOSITORIES: biostudies-literature