Pdm97, Least-Squares Fitting of the Molecular Electrostatic Potential With Net Atomic Charges and/or Multipoles
Reliable net atomic charges/multipoles can be found by fitting the molecular electric potential with program pdm97. The program provides a choice of geodesic(1), Connolly(2), cubic(3), or user specified grid points for the electric potential. The program includes calculation of hyperbolic-restricted charge magnitudes(4). In addition to net atomic charges, the program also allows any combination of atomic dipoles/quadrupoles, bond dipoles, as well as the addition of lone pair electron sites if required. The program directly reads output files from Gaussian-92 and Gaussian-94 programs, and will accept edited input from any program which produces a molecular electric potential on a grid. Program pdm97 is the most complete and versatile software package available for this type of calculation.
Molecular interactions occur during host-substrate docking, cluster, and crystal formation - whenever molecules associate with one another. The energy and geometry of molecular association is determined by the force field. As a component of the force field, an accurate set of net atomic charges is required. Or, if higher accuracy is needed, pdm97 can make extensions to the net atomic charge model in a variety of ways.
A particularly useful feature of the program is the easy and transparent way in which fixed charges and charge dependency conditions are specified. By specifying appropriate charge dependencies (e.g., equal charges or equal sums of charges), chemical intuition can assist to produce charges which are transferable between related types of molecules or molecular ions. Hyperbolic- restricted charges are specifically designed to increase charge transferability. All charge calculation include a complete error treatment with standard deviations and correlations between variables.
(1) Spackman, M. A., "Potential Derived Charges Using a Geodesic Point Selection Scheme", J. Comput. Chem., 1996, 17, 1-18
(2) Connolly, M. L., "Solvent-accessible Surfaces of Proteins and Nucleic Acids", Science, 1983, 221, 709-713
(3) Williams, D. E., "Net Atomic Charge and Multipole Models for the Ab Initio Molecular Electric Potential", Rev. Comp. Chem., 1991, 2, 219-271.
(4) Bayly, C. L.; Cieplak, P.; Cornell, W. D.; Kollman, P. A., "A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model", J. Phys. Chem., 1993, 97, 10269-10280.
Dr. Donald E. Williams
Department of Chemistry
University of Louisville
Louisville, Kentucky 40292, USA
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