AMBER/OPLS force field

Jorgensen has parameterized by fitting properties of bulk liquids to Monte Carlo simulations to give the AMBER/OPLS force field (26,157, 158). Conceptually, one is attracted ly the use of liquids and their observable properties as constraints during the derivation of a force field that is destined to study the properties of solvated molecules. 

The AMBER/OPLS force field is implemented in MOIL [16] and is used throughout the calculations. No cutoffs were used for this small system, and the 1 4 scaling factor was 2 and 8 for electrostatic and van der Waals interactions. No constraints on fast vibration were used. However, the stochastic difference equation filters the bond vibrations anyway. In Fig. 7 we compare the energy content of the bond vibrations in Ssdel optimization with different step sizes. 

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. 

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-... 

Jorgensen et al. has developed a series of united atom intermolecular potential functions based on multiple Monte Carlo simulations of small molecules [10-23]. Careful optimisation of these functions has been possible by fitting to the thermodynamic properties of the materials studied. Combining these OPLS functions (Optimised Potentials for Liquid Simulation) with the AMBER intramolecular force field provides a powerful united-atom force field [24] which has been used in bulk simulations of liquid crystals [25-27],... 

Tel. 212-280-2577, e-mail sl model%cuchem.bitnet A user-friendly molecular modeling package for molecular mechanics and conformational searching of organic molecules, proteins, nucleic acids, and carbohydrates. AMBER-, MM2-, and MM3-like and OPLS force fields implicit solvation model. Reads Cambridge and Brookhaven PDB files. VAX, Convex, Alliant, Cray, and workstations. 

Sequence analysis and biomolecular modeling. PRO-SIMULATE for molecular simulations with GROMOS, AMBER, and OPLS force fields. PROQUANTUM for semiempirical (MOPAC) and ab initio (CADPAC) calculations via a graphical interface. 

It is beyond the scope of this short review to list every available molecular mechanics program. Only a selected few programs are mentioned here, without descriptive details of the potential functions, minimization algorithms, or comparative evaluations. Both the CHARMM and AMBER force fields use harmonic potential functions to calculate protein structures. They were developed in the laboratories of Karplus and Kollman, respectively, and work remarkably well. The CFF and force fields use more complex potential functions. Both force fields were developed in commercial settings and based extensively or exclusively on results obtained from quantum mechanics. Unlike the other molecular mechanics methods, the OPLS force field was parameterized by Jorgensen to simulate solution phase phenomena. 

The most rigorous dielectric continuum methods employ numerical solutions to the Poisson-Boltzmann equation [55]. As these methods are computationally quite expensive, in particular in connection with calculations of derivatives, much work has been concentrated on the development of computationally less expensive approximate continuum models of sufficient accuracy. One of the most widely used of these is the Generalized Born Solvent Accessible Surface Area (GB/SA) model developed by Still and coworkers [56,57]. The model is implemented in the MacroModel program [17,28] and parameterized for water and chloroform. It may be used in conjunction with the force fields available in MacroModel, e.g., AMBER, MM2, MM3, MMFF, OPTS. It should be noted that the original parameterization of the GB/SA model is based on the OPLS force field. 

Les-Algorithmes Parc d Innovation Batiment Euclide F-67400 Illkirch, France Tel. 33-88-67-89-00, fax 33-88-67-98-01 Sequence analysis and biomolecular modeling. PRO-SIMULATE for molecular simulations with GROMOS, AMBER, and OPLS force fields. PROQUANTUM for semiempirical (MOPAC) and ab initio (CADPAC) calculations via a graphical interface. FDCALC and ESCALC for electrostatics calculations. Also PC-PROT-t- (sequence analysis), PC-TAMMO-l- (protein-lipid modeling), and MASCA (statistics) for PC. 

An extensive reparameterization of the Coulomb and Leonard-Jones terms of the AMBER force field led to the development of the OPLS (see OPLS Force Fields) parameter set. In OPLS the majority of bond, angle, and torsion terms were kept at their standard AMBER values however, the atomic partial charges were empirically determined for small molecules and assumed to be transferable to larger molecules. This treatment of partial charge differs significantly from the approach used in AMBER, in which a unique set of partial charges is derived for each molecule from fitting to the quantum mechanical ESP. 

AMBER A Program for Simulation of Biological and Organic Molecules Atoms in Molecules CHARMM The Energy Function and Its Parameterization Force Fields A Brief Introduction Force Fields A General Discussion Force Fields CFF GROMOS Force Field Intensities of Infrared and Raman Bands OPLS Force Fields,... 

AMI AMBER A Program for Simulation of Biological and Organic Molecules CHARMM The Energy Function and Its Parameterization Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Divide and Conquer for Semiempirical MO Methods Electrostatic Catalysis Force Fields A General Discussion Force Fields CFF GROMOS Force Field Hybrid Methods Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Methods Mixed Quantum-Classical Methods MNDO MNDO/d Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Parameterization of Semiempirical MO Methods PM3 Protein Force Fields Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mecha-nics/Molecular Mechanics (QM/MM) SINDOI Parameterization and Application. 

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