AMBER software packages

Modifications of the various versions of the AMBER parameter sets are implemented in numerous commercial and academic software packages. They are often referred to as AMBER. In every case, the user should read the documentation provided critically, and check the implementation by comparing the results of the implementation with original data. 

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. 

HyperChem is the PC-based molecular modeling and simulation software package marketed by Hypercube Inc. (http //www.hyper.com). The program provides molecular mechanics (with MM +, AMBER, BIO+ (CHARMm), and OPLS force... 

There are several software packages available that perform molecular dynamics simulations, such as AMBER,S9 CHARMM, SYBYL, DISCOVER, and GROMOS. 3 These programs are written to facilitate the simulation of peptides and proteins in vacuo and in solution. Because of the CPU time required to carry out these simulations, programs that run on a PC are not plentiful. However, HyperChem does provide for molecular dynamics using an IBM PC (or compatible) with the 80386 or 80486 microprocessor. Molecular dynamics of small molecules can be done using Chem3D Plus. The user who... 

Figure 7 Three-dimensional structure of DNA hairpin d(GCGAAGC) determined using NMR data obtained on a C- and N-labeled molecule. NOE, dihedral, and RDC restrains were applied to refine the structure using molecular dynamics simulations using AMBER 7.0 software package.

Fig. 4 Native and hybrid protein folds after energy minimization with AMBER." All proteins drawn in the same colour have the same amino acid sequence. The four native folds are displayed along the diagonal. The first row has the conformations for protein IQLX (cyan), the second row has the conformations for IIOS (red), the third row has the conformations for lAAP (yellow) and the fourth row has the conformations for IIGD (green). Along each column, the non-native conformations are obtained by imposing the backbone fold, or part of the backbone fold, of the native structure in that column on to the backbone of the other proteins. Below each conformation is the value of its potential energy in kcal/mol. This figure was adapted from and made with the help of the software package Visual Molecular Dynamics (VMD). ...

The Amber force field (S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, J. Comp. Chem., 7 (1986) 230) was used within the Insightll 95.0/Discover 2.9.7 software package from Biosym/MSI, 9685 Scranton Road, San Diego, CA 92121- 2777. Force field parameters for standard residues are published in Weiner et al. see equation (1), Figure (1), and the appendix of Weiner et al. for details. 

AMOEBA has been implemented in several widely used software packages including TINKER, OpenMM, AMBER, and Force Field The AMOEBA polarizable force field was first implemented... 

A working model (Figure 154) based on the NMR results and routinely accessible calculations (AMBER force field, as implemented in the MacroModel software package) has been proposed. This model is based on two assumptions (1) the predominant rotamer around the bond between the benzylic C atom and the N atom is that in which the benzylic proton is eclipsed with the carbonyl group, and (2) one of the two nonhydrogen substituents at C(3) occupies the anti position, relative to the carbonyl group. 

There are several MM force fields available, such as OPLS [29], CHARMM [30], AMBER [31], GROMOS [32], MMFF [33], CVFF [34], to mention a few. Several of them have been combined with the QM calculation programs and used in the combined QM/MM molecular dynamics simulations. [12,15,35,36] In our own work we have combined either GAUSSIAN94 [24] or GAMESS [25] with our own simulation software which is the modified version of McMOLDYN [37] package to study solvation phenomena and radical systems [38,39]. 

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