In:
The Journal of Chemical Physics, AIP Publishing, Vol. 117, No. 3 ( 2002-07-15), p. 1363-1376
Abstract:
A parallel searching algorithm based on eigenvector-following is used to generate databases of minima and transition states for all-atom models of Ac(ala)12NHMe and Ac(ala)16NHMe. The AMBER95 force field of Cornell et al. [J. Am. Chem. Soc. 117, 5179 (1995)] is employed both with and without a simple implicit solvent. We use a master equation approach to analyze the dynamics of both systems, and relate the results to the potential energy landscapes using disconnectivity graphs. The low-lying regions of both energy landscapes are compared and found to be remarkably similar. α-helix formation occurs via an ensemble of pathways involving both the N- and C-termini. The global minima of the two systems are also located using the CHARMM22 force field of Mackerell et al. [J. Phys. Chem. B 102, 3586 (1998)] , for comparison with AMBER95.
Type of Medium:
Online Resource
ISSN:
0021-9606
,
1089-7690
Language:
English
Publisher:
AIP Publishing
Publication Date:
2002
detail.hit.zdb_id:
3113-6
detail.hit.zdb_id:
1473050-9
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