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

Thomas Evangelidis tevang3 at gmail.com
Thu Jun 17 04:28:14 CEST 2010

> 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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100617/f82b88fc/attachment.html>

More information about the gromacs.org_gmx-users mailing list