Derivation of a New Force Field for Crystal-Structure Prediction Using Global Optimization:  Nonbonded Potential Parameters for Hydrocarbons and Alcohols

Abstract

A new procedure has been developed for deriving accurate nonbonded potential parameters for crystal-structure prediction. The method consists of two steps. First, an initial set of potential parameters is derived by fitting to ab initio interaction energies of dimers. Second, this initial set is refined to satisfy the following criteria: the parameters should reproduce the observed crystal structures and sublimation enthalpies accurately; the observed crystal structure should correspond to the global or to one of the lowest-energy minima of the potential. These goals are achieved by applying our new global optimization-based method for deriving nonbonded potential parameters (J. Phys. Chem. B 2003, 107, 712), which consists of a force-minimization and a vector Monte Carlo [VMC] method, to information about the potential energy surface of the crystal. The procedure enables one to obtain the best possible set of parameters for crystal-structure prediction for a given form of the potential. The computed nonbonded parameters of the "6-exp-1" potential, derived by using the new procedure, are presented for aliphatic and aromatic hydrocarbons and alcohols.

Folding of the Villin Headpiece Subdomain from Random Structures. Analysis of the Charge Distribution as a Function of pH

“…Although the conformational search identifies conformations with low RMSD (, 3.4 Å ), the potential function used does not rank this conformation as the lowest-energy one. As was noted, 2 a new parameterization of the existing all-atom force-field (currently under investigation in our laboratory) 37 should improve the accuracy of the predictions.…”

Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

“…It is worth noting that other contributions to the total energy, such as coupling of the conformation with the state of ionization of the individual amino acids (proton-binding equilibrium) (51) or an estimation of the conformational entropy (52), were not taken into account in these simulations. Conceivably, incorporation of these components as well as a new parameterization of the existing all-atom force-field (53) should improve the accuracy of the predictions.…”

Origin of intrinsic 310‐helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field

“…4 for (Ile) 3 and (Leu) 3 ), which in all-atom force fields are usually in the repulsive region of the van der Waals interactions. 23 This hindrance is a cause of the growing stabilization of the -strand over helical conformation for pLeu, pVal, and pIle pseudopeptides as the chain length increases (Fig. 3).…”