ENCAD

The success of any molecular simulation method relies on the potential energy function for the system of interest, also known as force fields [27]. In case of proteins, several (semi)empirical atomistic force fields have been developed over the years, of which ENCAD [28,29], AMBER [30], CHARMM [31], GRO-MOS [32], and OPLSAA [33] are the most well known. In principle, the force field should include the electronic structure, but for most except the smallest systems the calculation of the electronic structure is prohibitively expensive, even when using approximations such as density functional theory. Instead, most potential energy functions are (semi)empirical classical approximations of the Born-Oppenheimer energy surface. 

Levitt [177] Segmod module in Look Segment matching to PDB ENCAD force field, including vdW + Hbonds... 

Monte Carlo simulation to choose segments from PDB to model each side chain, followed hy averaging energy minimization with ENCAD 8 proteins rebuilt from Ca positions 80% correct... 

ENCAD 35 P2 P2 imp. 12-6 charge none proteins, nucleic acids... 

ENCAD M. Levitt, M. Hirshberg, R. Sharon, V. Daggett, Comp. Phys. Commun., 91 (1995), 215 ... 

Uhle, F., 2006. ENCAD, Incorporated. Gale Directory of Company Histories [WWW Document]. Available at http //www.answers.com/topic/encad-inc (accessed 11.08.13). 

Levitt et al. used high-temperature (498 K) simulations to study the unfolding of fragment B of protein A using the ENCAD force field and with an explicit treatment of solvent. Their simulations indicate that the protein adopts a compact denatured state within a few nanoseconds, with Helix in being the last element to unfold. Daggett et al. infer that Helix III... 

The ENCAD (energy calculations and dynamics) force field has been developed by Levitt et al. for the molecular dynamics simulations of proteins and nucleic acids in solution. It employs all-atom force field parameters. For condensed phase simulations the new three-center, flexible water model has been developed. The stress has been laid on the energy conservation effect during molecular dynamics simulations without coupling simulated systems to the thermal bath. The following expression has been used to calculate potential energy of the molecular systems ... 

The ENCAD force field has been mainly used for protein simulations but some limited applications to nucleic acids have also been reported DNA dodecamer. Tip rep-DNA, and Homeo rep-DNA complexes. The quality of this force field and its performance in the nucleic acid simulations are yet to be confirmed. One of the problems with this force field, which could be noticed here, is for example the irreversible base pair opening in DNA observed during molecular dynamics simulations. ... 

We use the ENCAD macromolecular potential model with the F3C water model. The combined model explicitly represents all of the atoms with the protein, allowing for dynamic freedom of all the atoms. The balance in explicit description and flexibility between the solute and solvent avoids the inadvertent introduction of unexpected and undetected systematic error into the simulations. This is especially problematic in simulations of biological macromolecules for which there are relatively few experimental observations available for calibration and testing. 

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