Molecular mechanics AMBER

Tel. 800-424-9737, fax 415-491-8311 (U.S.A.), tel. 41-38-337633 (U.K.) Model building, display, charge density, electrostatic potential, and molecular orbital plots. Stick, sphere, and dot surface display. 2D to 3D conversion. Protein and DNA fragment libraries. MM+, BIO+ (implementations of MM2 and CHARMM, respectively), OPLS, and AMBER molecular mechanics and dynamics. Solvent box. Semiempirical calculations by Extended Hiickel, CNDO, INDO, MINDO/3, MNDO, AMI, and PM3. Originated at Hypercube, Inc. (Dr. N. Ostlund et al.), of Ontario, Canada. Runs under Windows on a 386 or 486 PC and under Motif on a Silicon Graphics workstation. 

AMBER - molecular mechanics program and force field developed by Kollman s group [10]... 

TlypcrC hcm oilers four molecular mechanics force fields MM+, AMBER, BIO+, and OPES (sec References on page 106). To run a molecular mechanics calciilaLion. yon miisi lirsi choose a force Eeld. The following sections discuss considerations in choosing a force field. 

Hach molecular mechanics method has its own functional form MM+. AMBER, OPL.S, and BIO+. The functional form describes the an alytic form of each of th e term s in th e poteri tial. For exam pie, MM+h as both a quadratic and a cubic stretch term in th e poten tial whereas AMBER, OPES, and BIO+ have only c nadratic stretch term s, I h e functional form is referred to here as the force field. For exam pie, th e fun ction al form of a qu adratic stretch with force constant K, and equilibrium distance i q is ... 

An N-atom molecular system may he described by dX Cartesian coordinates. Six independent coordinates (five for linear molecules, three fora single atom) describe translation and rotation of the system as a whole. The remaining coordinates describe the nioleciiUir configuration and the internal structure. Whether you use molecular mechanics, quantum mechanics, or a specific computational method (AMBER, CXDO. etc.), yon can ask for the energy of the system at a specified configuration. This is called a single poin t calculation. ... 

Assisted model building with energy refinement (AMBER) is the name of both a force field and a molecular mechanics program. It was parameterized specifically for proteins and nucleic acids. AMBER uses only five bonding and nonbonding terms along with a sophisticated electrostatic treatment. No cross terms are included. Results are very good for proteins and nucleic acids, but can be somewhat erratic for other systems. 

The molecular mechanics force fields available include MM+, OPLS, BIO+, and AMBER. Parameters missing from the force field will be automatically estimated. The user has some control over cutoff distances for various terms in the energy expression. Solvent molecules can be included along with periodic boundary conditions. The molecular mechanics calculations tested ran without difficulties. Biomolecule computational abilities are aided by functions for superimposing molecules, conformation searching, and QSAR descriptor calculation. 

AMBER (assisted model building with energy refinement) a molecular mechanics force field... 

This discussion focuses on the individual components of a typical molecular mechanics force field. It illustrates the mathematical functions used, why those functions are chosen, and the circumstances under which the functions become poor approximations. Part 2 of this book. Theory and Methods, includes details on the implementation of the MM-t, AMBER, BlO-t, and OPES force fields in HyperChem. 

This difference is shown in the next illustration which presents the qualitative form of a potential curve for a diatomic molecule for both a molecular mechanics method (like AMBER) or a semi-empirical method (like AMI). At large internuclear distances, the differences between the two methods are obvious. With AMI, the molecule properly dissociates into atoms, while the AMBERpoten-tial continues to rise. However, in explorations of the potential curve only around the minimum, results from the two methods might be rather similar. Indeed, it is quite possible that AMBER will give more accurate structural results than AMI. This is due to the closer link between experimental data and computed results of molecular mechanics calculations. 

Quantum mechanical calculations generally have only one carbon atom type, compared with the many types of carbon atoms associated with a molecular mechanics force field like AMBER. Therefore, the number of quantum mechanics parameters needed for all possible molecules is much smaller. In principle, very accurate quantum mechanical calculations need no parameters at all, except fundamental constants such as the speed of light, etc. 

This term is essential to obtain the correct geometry, because there is no Pauli repulsion between quantum and classical atoms. The molecular mechanics energy tenn, E , is calculated with the standard potential energy term from CHARMM [48], AMBER [49], or GROMOS [50], for example. 

The energy functions for folding simulations include atom-based potentials from molecular mechanics packages [164] such as CHARMM [81], AMBER [165], and ECEPP... 

The GEMM software on the ST-100 is not a stand-alone package, and it requires a front-end simulation software package that runs on the host to provide data and to send command requests. It was designed and written with CHARMM (Chemistry at HARvard Macro-molecular Mechanics) (14) as the primary front-end, but additional software packages, such as AMBER (15), have subsequently been modified to drive GEMM. 

D. M. Ferguson, G. L. Seibel, and P. A. Kollman, AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules, Comp. Phys. Comm. 91 1 (1995). 

---