[gmx-users] Energy minimization: problems with ramachanrad score

Lucio Ricardo Montero Valenzuela lucioric at ibt.unam.mx
Thu Jun 17 06:41:14 CEST 2010

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 <tevang3 at gmail.com>:

> >
> > 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

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