Amber chemistry

Mills, J.S., White, R. and Gough, LJ. (1984/85). The chemical composition of Baltic amber. Chemistry and Geology 47 15-39. 

Caution If you are new to computational chemistry, do not use United Atoms for AMBER calculations. This HyperChem option is available for researchers who want to alter atom types and parameters for this force field. 

Note The BIO+ force field is an implementation of the CHARMM (Chemistry at HARvard Macromolecular Mechanics) force field developed in the group of Martin Karplus at Harvard University. Like AMBER and OPLS, it is primarily designed to explore macromolecules. 

The chemical environment for an atom in a molecule is probably unique to that molecule. Chemistry tries to find unifying concepts and the atom type is one of those unifying concepts. For example, the AMBER force field defines five atom types for oxygens ... 

Thermal neutron activation analysis has been used for archeological samples, such as amber, coins, ceramics, and glass biological samples and forensic samples (see Forensic chemistry) as weU as human tissues, including bile, blood, bone, teeth, and urine laboratory animals geological samples, such as meteorites and ores and a variety of industrial products (166). 

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. 

Wang, J., Wolf R.M., Caldwell, J.W, Kollman, P.A. and Case, D.A. (2004) Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157-1174. 

The molecular mechanics method is extremely parameter dependent. A force field equation that has been empirically parameterized for calculating peptides must be used for peptides it cannot be applied to nucleic acids without being re-parameterized for that particular class of molecules. Thankfully, most small organic molecules, with molecular weights less than 800, share similar properties. Therefore, a force field that has been parameterized for one class of drug molecules can usually be transferred to another class of drug molecules. In medicinal chemistry and quantum pharmacology, a number of force fields currently enjoy widespread use. The MM2/MM3/MMX force fields are currently widely used for small molecules, while AMBER and CHARMM are used for macromolecules such as peptides and nucleic acids. 

Most force fields used in coordination chemistry, in respect of the organic part of the molecules, are based on or are at least similar to the MM2 11 or AMBER 11 parameterization schemes, or mixtures thereof. However, it is of importance to stress again that transferring parameters from one force field to another without appropriate checks is not valid. This is not only a question of the different potential energy functions that may be used, but it is also a consequence of the interrelatedness of the entire set of parameters. Force field parameters imported from any source, whether a well-established force field or experimental data, should only be used as a starting point for further parameter refinement. 

Taylor, W.G., Zaman, M.S., Mir, Z., Mir, P.S., Acharya, S.N., Mears, G.J. and Elder, J.L. (1997) Analysis of steroidal sapogenins from amber fenugreek (Trigonella foenum-graecum) by capillary gas chromatography and combined gas chromatography/mass spectrometry. Journal of Agricultural and Food Chemistry 45(3), 753-759. 

Amber Research Laboratory, Department of Chemistry, Vassar College, Poughkeepsie, NY 12601... 

---