Potential energy function ECEPP

Let us consider Met-enkephalin (Tyr-Gly-Gly-Phe-Met) with 75 atomic sites in three different solvents including water. The model of a wee ter molecule is the extended simple point charge (SPG/E) model [19]. It is assumed that the peptide is immersed in the solvent at infinite dilution. The potential-energy functions and parameters are adopted from KONF90 [20] that is based on ECEPP/2 [21]. The peptide and solvent molecules comprise the interaction sites (atoms). The interaction between the peptide molecule and a water molecule is expressed as the sum of the site-site pair interactions that have the form... 

The energy functions for folding simulations include atom-based potentials from molecular mechanics packages [164] such as CHARMM [81], AMBER [165], and ECEPP... 

Figure 5. Potential energy as a function of time for the octa-peptide simulation at 300K starting from (a) an a-helix, and (b) from a structure provided by ECEPP.

For a significant portion of this work, the ECEPP/3 (Empirical Conformational Energy Program for Peptides) [38] potential model is utilized. In this force field, it is assumed that the covalent bond lengths and bond angles are fixed at their equilibrium values. Then, the conformation is only a function of... 

The ECEPP-05 force field (Arnautova et al. 2006 and references therein) is adjusted to both new experimental data and quantum mechanical results. Like previous ECEPP force fields ECEPP-05 utilizes the fixed bond lengths and bond angles but has some distinctive features as compared to both ECEPP/3 version and many other popular force fields. The van der Waals term of the energy is modeled by using the 6-exp potential function... 

Several empirical potential functions are used to calculate the conformational energy of a polypeptide. The one in most frequent use in our laboratory is ECEPP (Empirical Conformational Energy Program for Peptides)(Momany et al., 1975 Pottle et al., 1980). It was parameterized (Momany et al., 1974a) and tested (Momany et al., 1974b) on the crystals listed in Table 1 of a paper by Scheraga (1974) and on gas-phase data (Momany et al.. 

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