Transformation of the dihedral corrective map for d -amino residues using the CHARMM force field

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 (φ, ψ)→(−φ, −ψ) 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.