Re: [AMBER] strategies to speed up MM/GBSA screening

From: Jason Swails <>
Date: Thu, 14 Jul 2016 16:22:34 -0400

On Thu, Jul 14, 2016 at 10:29 AM, Thomas Evangelidis <>

> ​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 M. Swails
AMBER mailing list
Received on Thu Jul 14 2016 - 13:30:02 PDT
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