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Zap Details Dialog Box

Units

radios: {kT|kcal/mol}

Choose the units for Zap results: either kT (where k is Boltzmann's constant and T is temperature in K) or kcal/mol (calculated assuming T = 298.15 K).

Dielectric Model

menu: {Molecular|Accessible|Gaussian}

This controls the most important model decision, i.e. how to determine the dielectric values put on the grid. They fall into two models, discrete and continuous. the discrete can be of two types: Molecular and Accessible. In the third case the dielectric is determined via a Gaussian function. (See Theory chapter for more information.)

Probe Radius

field

This is the radius for the "Probe Atom", and is only active if Dielectric Model is Accessible. The default, 1.4 A, is the radius for water.

Convergence: Maximum Iterations

text

The Poisson-Boltzmann is solved by iteration; this is the maximum number of iterations to allow for completion.

Convergence: Energy Gradient

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The Poisson-Boltzmann is solved by iteration; this is the convergence criterion, in terms of grid energy, that will terminate the solution.

Zap VDW radius for H

radios: {Default Sybyl|Set to Zero|User Defined}

In some Zap calculations there may be an advantage to set the Van der Waal radius for hydrogen to zero or some other value.

H VDW radius

text

This text box is active if User Defined is selected as Zap VDW radius for H.

Zap Salt Concentration

radios: {Zero (no salt)|Physiological (0.125 M)|User Defined}

This parameter allows you to set the Ionic strength of the solution environment for Zap electrostatic calculations. The default is Zero (no salt). Choosing Physiological sets the Ionic Stength to 0.125 M; alternatively you can set an arbitrary (User Defined) value.

Ionic Strength

text

This text box is active if User Defined is selected as Zap Salt Concentration.