An integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described. The graphically controlled, atom‐based system allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state‐of‐the‐art molecular mechanics on any subset of up to 1,000 atoms. The system semiautomates the graphical construction and analysis of complex structures ranging from polycyclic organic molecules to biopolymers to mixed molecular complexes. We have placed emphasis on providing effective searches of conformational space by a number of different methods and on highly optimized molecular mechanics energy calculations using widely used force fields which are supplied as external files. Little experience is required to operate the system effectively and even novices can use it to carry out sophisticated modeling operations. The software has been designed to run on Digital Equipment Corporation VAX computers interfaced to a variety of graphics devices ranging from inexpensive monochrome terminals to the sophisticated graphics displays of the Evans & Sutherland PS300 series.
Atomic Born radii (α) are used in the generalized Born (GB)
equation to calculate approximations to the
electrical polarization component (G
pol) of
solvation free energy. We present here a simple analytical
formula
for calculating Born radii rapidly and with useful accuracy. The
new function is based on an atomic pairwise
r
ij
-4
treatment and contains several empirically determined parameters that
were established by optimization
against a data set of >10 000 accurate Born radii computed
numerically using the Poisson equation on a
diverse group of organic molecules, molecular complexes, oligopeptides,
and a small protein. Coupling this
new Born radius calculation with the previously described GB/SA
solvation treatment provides a fully analytical
solvation model that is computationally efficient in comparison with
traditional molecular solvent models
and also affords first and second derivatives. Tests with the
GB/SA model and Born radii calculated with
our new analytical function and with the accurate but more
time-consuming Poisson−Boltzmann methods
indicate that comparable free energies of solventlike dielectric
polarization can be obtained using either method
and that the resulting GB/SA solvation free energies compare well with
the experimental results on small
molecules in water.
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