OPLS/AA force fields

Thomas et al. [90] investigated the reaction catalyzed by neuraminidase from influenza virus. QM/MM calculations were performed using AMI in the QM part and treating the MM region with either the CHARMM22 [97] or OPLS-AA force fields [98]. 

Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., Jorgensen, W.L. Evaluation and reparametriza-tion of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 2001, 105, 6474-87. 

Careful consideration was taken in the parameterization process to insure that the parameters were deemed reasonable for the atom types, using the OPLS-AA force field atom types as a comparison. As one of the goals of this project was to ensure that robustness was achieved in many different calculated properties of the newly developed model, several sets of simulations were also performed to ensure that the parameters could achieve a reasonable agreement with experiment. Some of the properties calculated included the gas phase density, the partial molar volume in aqueous solution, and the bulk solvent structure as well. The calculation of the solubility was discussed in the previous section for the parameterization process and the viewing of these results, the solubility will be reported in log S values, as many of the literature values are reported as log S values, and therefore, the comparison would not lose any sensitivity due to rounding error from the log value. 

Sambasivarao, S.V., Acevedo, O. Development of OPLS-AA force field parameters for 68 unique ionic liquids. J. Chem. Theory. Comput. 2009, 5,1038-50. 

The CLAP model was built based on the OPLS-AA force field [21] functional form which means that, technically, it is easy to combine any molecule or residue already defined in the OPLS-AA database with the structures developed for ionic... 

The similar MM-GBSA approach has been shown to improve early enrichment rates in the virtual screening of large compound databases [66[. Again, the authors applied only simple energy minimization using the OPLS-AA force field [73] with the generalized Born implicit solvent model. 

Xu, Z., Luo, H.H., Tieleman, D.P. Modifying the OPLS-AA force field to improve hydration free energies for several amino add side chains using new atomic charges and an off-plane charge model for aromatic residues, J. Comp. Chem. 2007,28, 689-97. 

An alternative way to treat the surrounding protein is by including it in a MM description. All QM/MM calculations in this review are made with the program Qsite [34, 35, 36]. In this program the QM/MM interface is built by frozen localized molecular orbitals. Only predefined cuts between MM and QM parts are allowed. The QM parts of the QM/MM models therefore include the entire residue side chains. The MM part in a Qsite approach is treated with the OPLS-AA force field [37]. A dimer of the yeast enzyme consists of more than 8,000 atoms, which is the maximum number of atoms that Qsite can handle. To reduce the size of the MM part below this Hmit, parts of the second chain (B) that are more than 10 A away from the substrate are removed as well as the entire C and D chains. To keep the overall structure of the enzyme, approximately 40 atoms located close to the surface are kept frozen during the optimizations. The QM/MM treatment does not include dynamics and minima are located by optimizations starting from the X-ray structure. 

Kahn, K., and Bruice, T. C. [2002], Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides, J. Comput. Chem. 23, pp. 977-996, doi 10.1002/jcc.l0051. 

OPLS. The OPLS force field [23-25] was introduced in the early 1980s to simulate liquid-state properties of water and more than 40 organic liquids. The form of the OPLS-AA force field is given as [25]... 

The optimized potentials for liquid simulations (OPLS) force field can be divided into the OPLS-UA (united-atom) [96, 110-112] and the OPLS-AA (all-atom) [57, 67, 92, 103, 135-139] versions. Among the two, the OPLS-UA force field is predominantly used for engineering applications, mainly because it is computatirMi-ally cheaper than the all-atom version. The OPLS-UA force field is available for hydrocarbons [96], amides [110], peptides [110], alcohols [111], or proteins [112]. The OPLS-AA force field was parameterized for small organic molecules and is intended for biochemical applications. The parameters of the OPLS-AA force field are available for a broader range of functional groups and molecules. Thus, besides hydrocarbons [103] and alcohols [57], parameters can be found for thiols [57], sulfides [57], ketones [57], amides [57], amines [139], pyrrole [138], furan [138], diazoles [138], oxazoles [138], proteins [67], and carbohydrates [92], among others. 

Kony D, Damm W, Stoll S et al (2002) An improved OPLS-AA force field for carbohydrates. J Comput Chem 23 1416-1429... 

Jorgensen, W. L. Schyman, P. 2012. Treatment of halogen bonding in the OPLS-AA force field application to potent anti-HIV agents. J. Chem. Theory Comput. 8 3895-3901. 

Results of gas-phase optimizations with the OPLS-AA force field for complexes of the halide ions with several Brpnsted acids are summarized in Table 1. The optimal structures feature the expected hydrogen bonds, as illustrated for urea and pyrrole in Figure 2. The interaction energies for the ions with a TIP4P water molecule in Table 1 are essentially identical to the corresponding enthalpy changes from the mass spectrometry measurements of Kebarle and co-workers, namely, -23.3, -13.1, -12.6, and -10.2 kcal/mol for F, Cl, Bf, and F." Proper comparison requires conversion of... 

The MM subsystem was prepared in the following way. First, 500 water molecules represented with SPC/E model were contained within a cubic simulation box with periodic boundary conditions. The size L of the simulation box was, then, adjusted to reproduce the density 1.0 cm of water in ambient condition, which led to L = 24.6 A. To embed a solute molecule into the solvent we removed solvent molecules of which total volume amounts approximately to that of the solute. The molecular volumes of the solutes were those estimated in the standard PCM calculations [84] in Gaussian 09 with B3LYP/aug-cc-pVDZ level of theory. As a result the number of water molecules in the box was reduced to 496 499 according to the size of the solute molecule. The van der Waals interactions between solutes and solvent molecules were calculated using the OPLS-AA force field [85]. 

---