AMBER calculations

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. 

One notes that the results of QM MM MM depend sensitively on the choice of the charges used in the Amber calculation. The use of the Mulliken charges, for instance, in QM MM MM increases the error from —47 kcal/mol with RESP charges to -86 kcal/mol. This implies that the results will also depend sensitively on how to arbitrarily scale the near-border charges for the QM-MM interaction, because the problematic QM-MM boundary is very close to the reaction center. 

E. Brunet, A. M. Poveda, D. Rabasco, E. Oreja, L. M. Font, M. S. Batra, J. C. Rodrigues-Ubis, New Chiral Crown Ethers derived from Camphor and Their Application to Asymmetric Michael Addition. First Attempts to Rationalize Enantioselection by AMI and AMBER Calculations , Tetrahedron Asymmetry 1994, 5, 935-948. 

On the methodological side, it is gratifying to note, once these computer time consuming CP-MD calculations have been performed, that rapid classical dynamics AMBER calculations on the 18C6-H20 hydrate essentially yield similar qualitative conclusions instability of the Q hydrate, and "waltzing dynamics" of H20 over the D3d crown, which also validates early and subsequent force field studies, also pointing out the limitations of static views, even obtained by sophisticated quantum calculations. 

Figure 6.6 SPM (M,M,M)-120 and the structure of the dimer from Amber calculations [92]. Reprinted with permission from Org. Lett. 2001, 3, 1097-1099. Copyright 2001 American Chemical Society.

Figure 2 Optimized bond lengths (in A) for THR1 and THR2 in Crambin. Bold roman corresponds to the LSCF (RHF 6-31G /AMBER) calculation in which the quantum part is THR1. Light roman corresponds to the pure MM calculation and italic corresponds to crystallographic data. X is the QM frontier atom and Y is the MM frontier atom.

N is the number of point charges within the molecule and Sq is the dielectric permittivity of the vacuum. This form is used especially in force fields like AMBER and CHARMM for proteins. As already mentioned, Coulombic 1,4-non-bonded interactions interfere with 1,4-torsional potentials and are therefore scaled (e.g., by 1 1.2 in AMBER). Please be aware that Coulombic interactions, unlike the bonded contributions to the PEF presented above, are not limited to a single molecule. If the system under consideration contains more than one molecule (like a peptide in a box of water), non-bonded interactions have to be calculated between the molecules, too. This principle also holds for the non-bonded van der Waals interactions, which are discussed in Section 7.2.3.6. 

United Atom force fieldsare used often for biological polymers. In th esc m oleciiles, a reduced ii nm ber of explicit h ydrogen s can have a notable effect on the speed of the calculation. Both the BlOn and OPLS force fields are United Atom force fields. AMBER con tain s both aU nited and an All Atom force field. 

This section descrihes IlyperChem s four force fields, MM-h AMBER, OPES, and BlO-h providing auxiliary information for all force field calculations. 

OPTS (Optim i/.ed Potentials for Liquid Simulations) is based on a force field developed by the research group of Bill Jorgensen now at Yale University and previously at Purdue University. Like AMBER, the OPLS force field is designed for calculations on proteins an d nucleic acids. It in troduces non bonded in leraclion parameters that have been carefully developed from extensive Monte Carlo liquid sim u lation s of small molecules. These n on-bonded interactions have been added to the bonding interactions of AMBER to produce a new force field that is expected to be better than AMBER at describing simulations w here the solvent isexplic-... 

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. ... 

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. 

HyperChem offers four molecular mechanics force fields MM+, AMBER, BIO+, and OPLS (see References on page 106). To run a molecular mechanics calculation, you must first choose a force field. The following sections discuss considerations in choosing a force field. 

Another difference between the force fields is the calculation of electrostatic interactions. AMBER, BIO+, and OPLS use point charges to model electrostatic interactions. MM+ calculates electrostatic interactions using bond dipoles. The bond dipole method may not adequately simulate very polar or charged systems. 

Also use constant dielectric for MM+ and OPLS calculations. Use the distance-dependent dielectric for AMBER and BlO-t to mimic the screening effects of solvation when no explicit solvent molecules are present. The scale factor for the dielectric permittivity, 8, can vary from 1 to 80. HyperChem sets 8 to 1.5 for MM-t. Use 1.0 for AMBER and OPLS, and 1.0-2.5 for BlO-t. 

AMBER, BIO-h and OPES calculations use information on atomic charges. Atomic charges can come from these sources ... 

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. 

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. 

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. 

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