Hi again Braden (apparently I "followed" you here from the NAMD list),
QM/MM alchemical calculations with AMBER have indeed been done before, but
I'm not sure where (or if) they have been published. I might regard that
facility as experimental and thus the workflow (i.e. TI versus BAR, etc) is
largely DIY. Last I attempted this with SANDER and SQM I recall
re-purposing the TI output, but only after some careful error checking to
be sure the energies made sense. Probably the most recommendable path is to
first compute an MM solvation free energy and then a MM -> QM/MM
"correction".
HTH,
BKR
On Tue, Nov 27, 2018 at 3:10 AM Braden Kelly <bkelly08.uoguelph.ca> wrote:
> Hello,
>
>
> Amber documentation covers Free Energy calculations, such as thermodynamic
> integration and using other methods such as BAR. It independently discusses
> QM/MM as well. However free energy calculations, specifically alchemical
> changes in which a molecule is decoupled from the system, or mutated into
> another molecule, using a lambda parameter that changes from 0 to 1 or vice
> versa, are not discussed in the context of QM/MM.
>
>
> There is a post in the mail list from 2010 regarding TI when using QM/MM.
> There was an issue, but the issue wasn't that TI couldn't be done in QM/MM.
> This has me hopeful.
>
>
> Can free energy methods such as TI, BAR, etc. be performed in a QM/MM
> simulation in amber 18?
>
>
> I am specifically interested in hydration free energies of small (<50
> atoms) organic molecules.
>
>
> Thanks,
>
>
>
> Braden Kelly
>
> PhD. Candidate, E.I.T
>
> University of Guelph
>
> Biophysics Interdisciplinary Group (BIG)
>
> "I feel more like I do now than I did when I first got here."
>
>
> [1495766834308_mini_wolf_noir.jpg]
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Received on Tue Nov 27 2018 - 09:00:02 PST
