Category Proteomics>Protein Structure/Modeling Systems/Tools

Abstract CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a general and flexible software application for modeling the structure and behavior of molecular systems.

It can be used for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations.

A variety of systems, from an individual organic molecule to a large oligomeric protein in its solvent environment, can be simulated.

CHARMM also provides great flexibility:

CHARMM uses an empirical energy function for energy minimization, molecular dynamics simulation, or vibrational analysis.

With these major operations, CHARMM can efficiently calculate a wide range of molecular properties from simple peptide conformations to dynamic hinge-bending motions of large protein subunits.

Moreover, intermolecular problems that underlie structure-activity relationships such as enzyme-substrate or receptor-ligand binding interactions can be addressed.

The results of these calculations can be comprehensively interpreted using CHARMMís extensive data analysis facilities.

CHARMM Energy minimization --

Energy minimization adjusts the structure of the molecule in order to lower the energy of the system.

For small molecules, a global minimum energy configuration can often be found; for large macromolecular systems, energy minimization allows one to examine the local minimum around a particular conformation.

For maximum flexibility in supporting diverse application requirements, CHARMM provides six (6) different iterative minimization methods that employ both first and second derivative techniques.

Energy minimization is often performed in order to relieve strain in experimentally obtained or averaged structures.

In addition, barrier crossing or internal rearrangement in very large macromolecules may be studied through a combination of minimization techniques and coordinate constraints.

CHARMM Molecular dynamics --

Molecular dynamics simulates the natural motion of the molecular system and produces a set of coordinates and velocities which are the atomic motions of the system over time.

Given the CHARMM calculated empirical energy field, molecular dynamic simulations are performed by classical mechanics in which the equations of motion derived from Newtonís second law are solved for all the atoms in a molecule.

CHARMM can carry out dynamic simulations on a full molecular system or on selected regions of the structure. The latter option is particularly useful for simulations of large macromolecules.

For analysis purposes, the data manipulated during a molecular dynamic calculation can be used to compute a variety of time series for selected properties of the whole system or for some of its components.

For example, the user can map the variance over time for such properties as the position of a particular atom, the energy of a set of dihedrals, velocity of an atom or the geometry of a selected dihedral.

In addition, for well-defined systems, more general properties such as the radius of gyration, the number density of the molecule and entropic effects can be calculated.

CHARMM Vibrational analysis --

Vibrational analysis generates normal mode vectors and computes vibrational frequencies and intensities. This technique provides an accurate local description of the potential energy surface.

The normal modes can also be used to interpret Infrared (IR) spectra or allow one to improve the force constant parameters by matching the experimental spectra.

Furthermore, analysis of the normal modes of large macromolecules can be used to elucidate the individual motional contributions to the overall dynamics of the system.

CHARMM Analysis facility --

An essential part of computing the behavior and properties of large molecular systems is an effective procedure for analyzing the results.

CHARMM has an extensive facility for analyzing structural data and the results of various calculations.

This analysis facility, in conjunction with the correlation function calculations, allows the user to create, manipulate, print and display tables of data generated by CHARMM, compare structures and calculations, manipulate any time series calculated during a dynamics calculation, and search for close contacts between atoms of an entire structure or parts of it.

CHARMM Computational capabilities --

Energy minimization, molecular dynamics and vibrational analysis form the core of CHARMMís computational capabilities.

In addition to these functions, a wide variety of other facilities are also provided. These include crystal structure simulations, stochastic and solvent dynamics, correlation functions, free energy calculations, user defined subroutines and other computational tools.

The entire CHARMM package can be used to address a wide range of problems in macromolecular structure and function.

The primary concern of CHARMM has been to create a research instrument for theoretical studies of the properties and biological function of molecules.

Consequently, emphasis has been placed on the versatility of the program and it is being continually modified as work proceeds into new areas.

CHARMMís Main features/capabilities:

1) CHARMM is a versatile and widely used molecular simulation program with broad application to many-particle systems;

2) It has been developed with a primary focus on the study of molecules of biological interest, including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments;

3) CHARMM provides a large suite of computational tools that encompass numerous conformational and path sampling methods, free energy estimates, molecular minimization, dynamics, and analysis techniques, and model-building capabilities;

4) It is useful for a much broader class of many-particle systems;

5) CHARMM can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models; and

6) It has been ported to numerous platforms in both serial and parallel architectures.

System Requirements

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Manufacturer Web Site CHARMM

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G6G Abstract Number 20715

G6G Manufacturer Number 104284