Development of glycyl radical parameters for the OPLS-AA/L force field.
On the basis of quantum chemical calculations C(alpha)-glycyl radical parameters have been developed for the OPLS-AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum-of-squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS-AA energies reproduced those calculated quantum chemically almost perfectly.
Komáromi
István
I
Thrombosis and Haemostasis Research Group, Hungarian Academy of Sciences, University of Debrecen, Debrecen H-4010, Hungary.
Owen
Michael C
MC
Murphy
Richard F
RF
Lovas
Sándor
S
D005609:Free Radicals / Q000737:chemistry*; D005998:Glycine / Q000737:chemistry*; D008962:Models, Theoretical; D011789:Quantum Theory
D005609:Free Radicals; D005998:Glycine