OPLS

OPES (Optimized 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 and nucleic acids. It introduces nonbonded interaction parameters that have been carefully developed from extensive Monte Carlo liquid simulations of small molecules. These nonbonded interactions have been added to the bonding interactions of AMBERto produce anew force field that is expected to be better than AMBER at describing simulations where the solvent is explic- 

The HyperChem OPLS force field gives results equivalent to the original OPLS force field. 

The OPLS force field is described in two papers, one discussing parameters for proteins [W. L. Jorgensen and J. Tirado-Rives, J. Amer. Chem. Soc., 110, 1657 (1988)] and one discussing parameters for nucleotide bases [J. Pranata, S. Wierschke, and W. L. Jorgensen, J. Amer. Chem. Soc., 113, 2810 (1991)]. The force field uses the united atom concept for many, but not all, hydrogens attached to carbons to allow faster calculations on macromolecular systems. The amino and nucleic acid residue templates in HyperChem automatically switch to a united atom representation where appropriate when the OPLS option is selected. 

The OPLS atom types are a superset of the AMBER united atom types and the bonding parameters are just those of AMBER, supplemented where needed by the OPLS developers. The bond stretch, angle bending, dihedral angle and improper dihedral angle terms are identical to those of AMBER. Unlike AMBER, different combination rules are used for the van der Waals parameters, no hydrogen bonding term is used and no lone pairs are used. 

The OPLS form of electrostatic interactions is that of equation (26) on page 179. That is, it uses a charge-charge interaction just like AMBER. However, since the nonbonded potentials were developed 

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W L. Jorgensen, OPLS force fields, in 77ie Encydopedia of Computational Chemistry, Vol. 3, P. v. R. Schleyer,... 

Th is discussion focuses on th e individual compon en ts of a typical molecular mechanics force field. It illustrates the mathematical functions used, wdi y those functions are chosen, and the circiim -Stan ces u n der wh ich the fun ction s become poor approxirn atiori s. Part 2 of th is book, Theory and Melhadx, includes details on the implementation of the MM+,. AM BHR, RlO-g and OPl.S force fields in HyperChem. 

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. 

Lsc th e force fields th at have dern on strated accuracy for particu lar molecules or simulations. For example, CiPLS reproduces physical properties in liquid simulations extremely well. MM+ reproduces the structure and thermodynamic properties of small, nonpolar molecules better than AMBER, BIO+, and OPLS. 

Also use constant dielectric Tor MM+aiul OPLS ciilciilatimis. Use the (lislance-flepeiident dielecinc for AMBER and BlO+to mimic the screening effects of solvation when no explicit solvent molecules are present. The scale factor for the dielectric permittivity, n. can vary from 1 to H(l. IlyperChem sets tt to 1. .5 for MM-r. Use 1.0 for AMBER and OPLS. and 1.0-2..5 for BlO-r. 

AMBER. BlO-t-. and OPLS calciilations use information on atomic charges. Atomic charges can come from these sources ... 

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 ... 

Atom VDWForm at cn try to SigmaKpsilori. rh e I 4 van der Waals interactions are nsnally scaled in OPLS to one-eighth their nominal value (a scale factor of (1.125 in the Porce Field Options dialog bo.x). 

A. rather complex procedure is used to determine the Born radii a values of which. calculated for each atom in the molecule that carries a charge or a partial charge. T Born radius of an afom (more correctly considered to be an effective Born radii corresponds to the radius that would return the electrostatic energy of the system accordi to the Bom equation if all other atoms in the molecule were uncharged (i.e. if the other ato only acted to define the dielectric boundary between the solute and the solvent). In Sti force field implementation, atomic radii from the OPLS force field are assigned to ec... 

Optimized potentials for liquid simulation (OPES) was designed for modeling bulk liquids. It has also seen significant use in modeling the molecular dynamics of biomolecules. OPLS uses five valence terms, one of which is an electrostatic term, but no cross terms. 

In order for this to work, the force field must be designed to describe inter-molecular forces and vibrations away from equilibrium. If the purpose of the simulation is to search conformation space, a force field designed for geometry optimization is often used. For simulating bulk systems, it is more common to use a force field that has been designed for this purpose, such as the GROMOS or OPLS force fields. 

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. 

The force field equations for MM+, AMBER, BIO+, and OPLS are similar in the types of terms they contain bond, angle, dihedral, van derWaals, and electrostatic. There are some differences in the forms of the equations that can affect your choice of 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. 

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. 

AMBER, BIO-h and OPLS scale 1 van der Waals and 1 electrostatic interactions. Although the value of the 1 nonbonded scale factors is an option in HyperChem, you should generally use recommended values. This is because during parameterization, the force field developers used particular values for the 1 nonbonded scale factors, and their parameters may not be correct for other scale factors. 

The van der Waals scale factors used during force field parameterization are 0.5 for AMBER, 1.0 for BlO-t, and 0.125 for OPLS. Eor 1-4 electrostatic interactions, use 0.5 for AMBER, BlO-t, and OPLS. 

Jorgensen, W.L. Tirado-Rives, J. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110 1657-1666, 1988... 

Choose the appropriate force field (MM-t, AMBER, OPLS, or BlO-t). 

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