Molecular Mechanics with HyperChem

Molecular Mechanics

HyperChem software is a versatile tool for exploring the structure and stability of molecules. HyperChem integrates several molecular mechanics methods and an extensive suite of visualization and analysis tools to provide a powerful, easy-to-use, desktop molecular modeling program.

HyperChem provides simple ways to produce 3D molecular structures on screen, a choice of four force fields, geometry optimization techniques to search for stable structures, and molecular dynamics techniques to carry out conformational searching and to investigate structural changes.

Molecular Mechanics Applications

HyperChem's molecular mechanics methods have many applications to the study of molecular structure and stability. Some typical applications are:

Calculating relative conformational energies of a series of analogous structures.
Re-optimizing a peptide after introducing a selective mutation.
Refining structures prior to more rigorous quantum mechanics calculations.
Assessing possible steric effects in a reactive intermediate.

To simulate the effects of solvent attenuation of electrostatic interactions, HyperChem offers a distance-dependent dielectric constant option for selected force fields.

Four Force Fields

HyperChem includes four built-in molecular mechanics force fields: new implementations of techniques developed and published by respected research groups.

MM+

Appropriate for most non-biological species.
Based on the MM2(1977) force field developed by N. L. Allinger.
Uses the 1991 parameter set.
Extended to incorporate nonbonded cutoffs, restraints, and periodic boundary conditions.
Computes default parameters for cases where MM2 parameters are not available.

AMBER

Appropriate for use on polypeptides and nucleic acids with all hydrogen atoms explicitly included.
The AMBER force field was developed by the research group of P. A. Kollman.
Includes parameters for Versions 2.0 and 3.0a of this widely-used force field.

OPLS

Designed for calculations on nucleic acids and peptides.
The OPLS united-atom force field was developed by the research group of W. L. Jorgensen.
The nonbonded interaction parameters are optimized for calculations where the solvent is explicitly included in the calculation.
Appropriate for use with HyperChem software's built-in periodic water box.

BIO+

Primarily designed to explore macromolecules.
Implements the CHARMM force field developed in the group of Martin Karplus.
Includes CHARMM parameters published for amino acids.
Allows users to add other parameter sets.

Adding Parameters

A recurring problem in working with molecular mechanics force fields is that of insufficient parameters. HyperChem tackles the problem by providing a default scheme for the MM+ force field and by allowing users to add their own parameters. All HyperChem force fields parameters are present as text files to which new atom types and new parameters can be easily added. The user can also define rules for automatic assignment of new atom types.

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