Paper Citing NAMD - Abstract
Turpin, Eleanor R.; Hirst, Jonathan D.
Transformation of the dihedral corrective map for D-amino residues using the CHARMM force field
CHEMICAL PHYSICS LETTERS, 543:142-147, AUG 10 2012
Molecular dynamics simulations in explicit solvent were performed on two peptides and two proteins containing D-amino residues, using three implementations of the CHARMM22 all-atom force field: (a) with the standard CMAP corrective term, (b) neglecting the correction entirely and (c) using a transformation of the CMAP grid (phi, psi) -> (-phi, -psi) for the D-amino residues. The transformed map led to sampling of conformations which are closest to the X-ray crystallographic structures for D-amino residues and the standard CMAP correction destabilises D-amino secondary structure. Thus, the transformation of the CMAP term is needed to simulate proteins and peptides containing D-amino residues correctly. (C) 2012 Elsevier B.V. All rights reserved.
