Paper Citing NAMD - Abstract
Stavrakoudis, Athanassios
Molecular dynamics simulations of an apoliprotein A-I derived peptide in explicit water
CHEMICAL PHYSICS LETTERS, 461:294-299, AUG 20 2008
Molecular dynamics simulations have been performed for the 104-117 alpha-helical fragment of apoliprotein A-I using the CHARMM22 force field and the NAMD simulation engine. Simulation ( 50 ns in explicit water) resulted in significant appearance of pi-helix conformation, which was totally diminished when the CMAP correction of the CHARMM force field was applied. This is consistent with other similar studies which suggest that the observation of pi-helix in peptide conformation was force field biased rather actually existed. This study suggests that the 104-117 fragment of apoliprotein A-I has a stable alpha-helical conformation in water. (C) 2008 Elsevier B.V. All rights reserved.
