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

[Thomas Evangelidis]

>
> 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.
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