On Thu, Jul 14, 2016 at 10:29 AM, Thomas Evangelidis <tevang3.gmail.com>
wrote:
> Thank you Jason and Carlos for your thorough explanation! I am sure this
> thread will help other people understand better how GB simulations work.
>
> .Jason
> In drug design the reviewers don't care if you could produce the correct
> docking poses (most of which are unknown anyway) or calculate accurate free
> energies of the thousands of compounds that you screened. They only care if
> you could increase the enrichment factor. Leaving only the binding pocket
> residues flexible is one of the usual tricks to achieve that. The reason
> why it works is outside the scope of this thread :)
>
Fair enough. It's still not a use-case that we've optimized. You're more
than welcome to give it a try, but the nature of GB will limit you to
~3-10x speedup at best :).
All the best,
Jason
--
Jason M. Swails
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Received on Thu Jul 14 2016 - 13:30:02 PDT
