Custom Search
-- Dr. Gabriel E. Jara Molecular Modeling Laboratory INQUIMAE - Instituto de Química-Física de Materiales, Ambiente y Energía DQIAyQF - Departamento de Inorgánica, Analítica y Química-Física FCEyN - Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Intendente Güiraldes 2160 - Hall 2, 1er piso. Ciudad Universitaria - C1428EGA Buenos Aires - Argentina Tel: +54 11 4576 3378 /79 /80, int. 123 ------ Gabriel, If the method does not converge, then it may simply not be suitable for the system you want to model. However, there are a lot of things that probably need to be additionally considered: 1.) The default AM1/d model (AM1/d-PhoT) was not designed for polyphosphates or nucleobases, as such ATP could be problematic on its own. Does it optimize sensibly in the gas phase? 2.) The QM region you describe is quite large, does a smaller system converge SCF? The Lysine sidechain in particular bothers me since AM1/d-PhoT was not parameterized with nitrogen in mind *at all*. 3.) The (default) Mg parameters from Imhof, et al. have NOT been extensively validated with AM1/d-PhoT. 4.) Perhaps trivial, but have you double checked your charge and link atom selections? This probably isn't an issue since other methods converge, but is usually my first goto when things go badly wrong. 5.) Also possibly trivial, but have you spent a lot of time optimizing the MM region? Putting sensible charges (gas phase mulliken perhaps?) and Lennard-Jones parameters on your QM region and then optimizing should help immensely if you haven't done that already. 6.) Probably not relevant until you do dynamics, but be sure to use the QM/MM switching function, as energy is otherwise not well conserved, especially with d-orbitals. This is not the default (for backwards compatibility only). Brian _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Jun 01 2012 - 07:30:02 PDT