Paper Citing NAMD - Abstract
Rai, B.K.; Prohofsky, E.W.; Durbin, S.M.
Single-atom test of all-atom empirical potentials: Fe in myoglobin
JOURNAL OF PHYSICAL CHEMISTRY B, 109:18983-18987, OCT 13 2005
The measured Fe vibrational density of states in deoxy-myoglobin, obtained from nuclear resonance vibrational spectroscopy, is compared to results from a normal-mode analysis using an all-atom empirical potential. Substantial disagreement reveals that for this one atom, the empirical potential does not accurately describe the actual forces. A Green function technique is developed to calculate the iron vibrational spectrum of deoxymyoglobin by coupling the independently calculated heme and globin normal modes; nonbonded interactions between the heme molecule and the protein are essential for a good fit to the measurements. A projection of the eigenvectors from this potential onto the displacements induced by binding of CO demonstrates that normal modes over a broad range centered around 50-150 cm(-1) may drive the ligand-induced structural changes.
