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Both molecular mechanical and quantum mechanical calculations play animportant role in describing the behavior and structure of molecules. In thiswork, we compare for the same peptide systems the results obtained from foldingmolecular dynamics simulations with previously reported results from quantummechanical calculations. More specifically, three molecular dynamicssimulations of 5 $\mu$s each in explicit water solvent were carried out forthree Asn-Gly-containing heptapeptides, in order to study their folding anddynamics. Previous data, based on quantum mechanical calculations and the DFTmethods have shown that these peptides adopt $\beta$-turn structures in aqueoussolution, with type I' $\beta$-turn being the most preferred motif. The resultsfrom our analyses indicate that for the given system the two methods diverge intheir predictions. The possibility of a force field-dependent deficiency isexamined as a possible source of the observed discrepancy.

plos one

On the propensity of Asn-Gly-containing heptapeptides to form  $\beta$-turn structures : comparison between ab initio quantum mechanical  calculations and Molecular Dynamics simulations