Hi Nick
Great question, but not really associated with Amber per-se.
David Mobley has a some nice reviews published discussing some of these
issues
(
https://github.com/MobleyLab/benchmarksets/blob/master/paper/benchmarkset.pdf)
There is no 'correct' answer to your question, and you should read that
review to start with.
adrian
On 8/15/17 9:36 AM, Nikolay N. Kuzmich wrote:
> Dear Amber user and developers,
>
> I would like to ask you how accurate are the TI calculations of ddG in Amber
> for different ligands bound to a protein?
> How large is the average deviation from the experimental data?
> How big can be structural difference between the ligands (e.g. number of
> heavy atoms)
> for the precision to remain acceptable?
> Any useful links to the topic are highly appreciated too.
>
> Thank you,
> Nick
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Aug 15 2017 - 09:00:03 PDT
