The implicit water models were built in a time when computing time was limiting because of the computing power if this epoch. But now is feasible to do simulations with explicit water. Maybe one should argue that at the first minimization of a protein waterbox the waters are not in the natural position, but there is not a natural position for a water, there is an ensemble of positions that we can explore with a MD. Minimization is to remove severe clashes between atoms, but the prediction of an homology model should end with an MD, and then one can get an average structure and minimize it, to get the homology model. Best regards. Lucio Montero PhD. student Insituto de Biotecnologia, UNAM, Mexico
Mensaje citado por Thomas Evangelidis <[email protected]>: > > > > Without having actually read their paper... there's could easily be a kind > > of apples-and-oranges comparison going on. The local optimum resulting from > > a single EM using MM forcefields optimized for non-vacuum conditions on > > near-native folds in vacuo are being compared with (say) crystal structures > > for the fitness of those minima as a model of (presumably) what's around > > under biological conditions. I'd guess that there's an appreciable number > of > > cases where this is a three-way absurdity... > > > > > With respect to the MM forcefields optimized for aqua conditions, isn't it > more reasonable to minimize the homology models in a waterbox? After all > that the native conformation is in aqua solution. > -- Lucio Ricardo Montero Valenzuela Estudiante de doctorado en Ciencias Bioquímicas Lab. del Dr. Federico Sánchez Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico ---------------------------------------------------------------- Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
