Force Field Options

The HyperChem Reference manual and Getting Started discuss the sequence of steps to perform a molecular mechanics calculation. These steps include choosing a force field, force field options, and possible restraints. 

You can use two types of dielectric functions a constant and a distance-dependent dielectric. Use constant dielectric for in vacuo systems and for molecular systems with explicit solvent molecules. 

Also use constant dielectric for MM+ and OPLS calculations. Use the distance-dependent dielectric for AMBER and BlO-t to mimic the screening effects of solvation when no explicit solvent molecules are present. The scale factor for the dielectric permittivity, 8, can vary from 1 to 80. HyperChem sets 8 to 1.5 for MM-t. Use 1.0 for AMBER and OPLS, and 1.0-2.5 for BlO-t. 

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I lle HIO+force field option in HyperChem hasno hydrogen bond-in g term, Th is is con sisten I with evolution andcommon useofthe CH.ARMM force field (even the 1983 paper did n ot usc a liydrogen boruiin g term in its exam pic calculation s an d men lion ed that the functional form used then was u n satisfactory and under review). 

Before running a molecular dynamics simulation with solvent and a molecular mechanics method, choose the appropriate dielectric constant. You specify the type and value of the dielectric constant in the Force Field Options dialog box. The dielectric constant defines the screening effect of solvent molecules on nonbonded (electrostatic) interactions. 

The functional form for van der Waals interactions in AMBER is identical with that shown in equation (13) on page 175. The coefficients A. and B.. are computed from the parameters in the file pointed to by the 6-12AtomVDW entry for the parameter set in the Registry or the chem. ini file, usually called nbd.txt(dbf), and optionally with the file pointed to by the 6-12PairVDW entry for the parameter set, usually called npr.txt(dbf). The standard AMBER parameter sets use equations (15) and (16) for the combination rules by setting the 6-12AtomVDWFormat entry to RStarEpsilon. The 1 van der Waals interactions are usually scaled in AMBER to half their nominal value (a scale factor of 0.5 in the Force Field Options dialog box). 

Chem.ini or Registry Setup of Force Field Options... 

Figure 14.8. Molecular mechanics calculation with HyperChem. Setup for MM calculation of lysozyme (pdb1 lyz.ent) includes selection of the method and options. The lower left inset displays dialog box for MM methods and the upper right inset shows dialog box for force field options.

The program FLAP fits ligand molecules into a set of GRID MIFs of a protein structure. Thus FLAP can be used as docking program, which uses all the GRID force fields options and capabilities. 

In Eqs. [15] and [16], D is the effective dielectric constant and is generally preset to a low value (1-1.5) to simulate the gas phase. However, most force fields optionally allow for a user-defined dielectric constant. In some force fields a distance-dependent dielectric constant (function) is used. In Eq. [16], and a describe the orientation of the bond dipoles, and x, and are the magnitudes of interacting dipoles i and /, respectively.22... 

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