Paper Citing NAMD - Abstract
Iori, F.; Di Felice, R.; Molinari, E.; Corni, S.
GoIP: An Atomistic Force-Field to Describe the Interaction of Proteins With Au(111) Surfaces in Water
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1465-1476, JUL 15 2009
A classical atomistic force field to describe the interaction of proteins with gold (111) surfaces in explicit water has been devised. The force field is specifically designed to be easily usable in most common bio-oriented molecular dynamics codes, such as GROMACS and NAMD. Its parametrization is based on quantum mechanical (density functional theory [DFT] and second order Moller-Plesset perturbation theory [MP2]) calculations and experimental data oil the adsorption of small molecules on gold. In particular, a systematic DFT survey of the interaction between Au(111) and the natural amino acid side chains has been performed to single out chemisorption effects. Van der Waals parameters have been instead fitted to experimental desorption energy data of linear alkanes and were also studied via MP2 calculations. Finally, gold polarization (image charge effects) is taken into account by a recently proposed procedure (Iori, F.; Corni, S. J Comp Chem 2008, 29 1656). Preliminary validation results of GoIP on an independent test set of small molecules show the good performances of the force field. (C) Wiley Periodicals, Inc. J Comput Chem 30: 1465-1476, 2009
