AMBER” force field

Fig. 1. The time evolution (top) and average cumulative difference (bottom) associated with the central dihedral angle of butane r (defined by the four carbon atoms), for trajectories differing initially in 10 , 10 , and 10 Angstoms of the Cartesian coordinates from a reference trajectory. The leap-frog/Verlet scheme at the timestep At = 1 fs is used in all cases, with an all-atom model comprised of bond-stretch, bond-angle, dihedral-angle, van der Waals, and electrostatic components, a.s specified by the AMBER force field within the INSIGHT/Discover program.

Finally, each force field may have multiple parameter sets (the val-uesolT oand K. for example). Th e AMBER force field and AMBER set ol types may be used with, for example, the AMBER/2 or AMDER/3 set of param eters. 

The chemical environment foran atom m a molecule is probably niiit iie to th at molecule. Chem istry tries to find unify in g concepts an d the atom type Is on e of those unifying con cepts. For example, the AMBER force field defines five atom types for oxygens ... 

Xote that two dilTcren t environni cn is. although they migh t be dis-liiignisbcd by tests (such as for ether and ester) can share an atom type (such as OS), A rel inem en i of th e AMBER force field would use separate types for these two along with differen t parani eters for th e differen L types. 

Many of the torsional terms in the AMBER force field contain just one term from the cosine series expansion, but for some bonds it was found necessary to include more than one term. For example, to correctly model the tendency of O-C—C-O bonds to adopt a gauche conformation, a torsional potential with two terms was used for the O—C—C—O contribution ... 

Fig. 4.S Variation in torsional energy (AMBER force field) with O-C-C-0 torsion angle (to) for OCH -CHjO fragment. The minimum energy conformations arise for to = 60° and 300°.

Fhe van der Waals and electrostatic interactions between atoms separated by three bonds (i.c. the 1,4 atoms) are often treated differently from other non-bonded interactions. The interaction between such atoms contributes to the rotational barrier about the central bond, in conjunction with the torsional potential. These 1,4 non-bonded interactions are often scaled down by an empirical factor for example, a factor of 2.0 is suggested for both the electrostatic and van der Waals terms in the 1984 AMBER force field (a scale factor of 1/1.2 is used for the electrostatic terms in the 1995 AMBER force field). There are several reasons why one would wish to scale the 1,4 interactions. The error associated wilh the use of an repulsion term (which is too steep compared with the more correct exponential term) would be most significant for 1,4 atoms. In addition, when two 1,4... 

Example For the AMBER force field, a carbonyl C-0 bond has an equilibrium bond length of 1.229 A and a force constant of 570 kcal/mol A . The potential for an aliphatic C-C bond has a minimum at 1.526 A. The slope of the latter potential is less steep a C-C bond has a force constant of 310 kcal/mol A. ... 

Example This example of an HN-C(O) amide torsion uses the AMBER force field. The Fourier component with a periodicity of one (n = 1) also has a phase shift of 0 degrees. This component shows a maximum at a dihedral angle of 0 degrees and minima at both -180 and 180 degrees. The potential uses another Fourier component with a periodicity of two (n = 2). 

The AMBER force field replaces the van der Waals by a 10-12 potential for pairs of atoms that can participate in hydrogen bonding (equation 12). The hydrogen bond potential does not contribute significantly to the hydrogen bonding attraction between two atoms rather, it is implemented to fine-tune the distances between these atoms. 

The attraction for two neutral atoms separated by more than four Angstroms is approximately zero. The depth of the potential wells is minimal. For the AMBER force field, hydrogen bonds have well depths of about 0.5 kcal/mol the magnitude of individual van der Waals well depths is usually less. 

Atom types are defined in the file chem.rul. The atom types for each of the force fields are listed in the files pointed to by the AtomTypeMass entries associated with the specific force fields in the Registry or the chem.ini file. They are usually named typ.txt or typ.dbf, depending on whether text or dBASE format is used. For the AMBER force field, all variations use the same type file, defined in the [Amber] section of the Registry or the chem.ini file. It is usually called ambertyp.txt, if a text format file is used, indicated by FileFormat=Text or ambertyp.dbf, if a dBASE III format file is used, indicated by FileFormat=dbf. 

Although interactions between vicinal atoms are nominally treated as nonbonded interactions, most of the force fields treat these somewhat differently from normal 1-5 and greater nonbonded interactions. HyperChem allows each of these nonbonded interactions to be scaled down by a scale factor <1.0 with AMBER or OPLS. For BlO-t the electrostatic may be scaled and different parameters may be used for 1 van der Waals interactions. Th e AMBER force field, for exam p le, norm ally u ses a scalin g factor of 0.5 for both van der Waals and electrostatic interactions. 

AMBER was first developed as a united atom force field [S. J. Weiner et al., J. Am. Chem. Soc., 106, 765 (1984)] and later extended to include an all atom version [S. J. Weiner et al., J. Comp. Chem., 7, 230 (1986)]. HyperChem allows the user to switch back and forth between the united atom and all atom force fields as well as to mix the two force fields within the same molecule. Since the force field was developed for macromolecules, there are few atom types and parameters for small organic systems or inorganic systems, and most calculations on such systems with the AMBER force field will fail from lack of parameters. 

The AMBERforce field expects lone pairs to be added to all sulfur atoms and computes the interactions as if these lone pairs were atoms with a specific type just like any other atom. The templates automatically add the expected lone pairs to sulfur atoms when usin g th e AMBER force field. 

Nucleotide atom-centred charges within the amber force field, J. Mol. Mod. 1 115 (1995). 

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