I don't have specific advice, but you might look into Michael Feig's
extensive work on using md to refine structure models.
On Wed, Dec 29, 2021, 1:39 PM Matthew Guberman-Pfeffer <
matthew.guberman-pfeffer.uconn.edu> wrote:
> Dear Amber Community,
>
> I’m wondering if advice can be offered on how to select the maximum
> temperature and heating/cooling schedules for simulated annealing.
> I’m thinking of using simulated annealing for the below purpose; if a
> different approach seems more appropriate, I’d appreciate those suggestions
> as well.
>
> I have an AlphaFold-predicted protein into which several porphyrin-type
> cofactors were inserted. The geometry of the system is much improved after
> minimization, but some backbone motion is still needed to alleviate the
> strain between two of the porphyrin rings (e.g. one ring is very buckled to
> accommodate the substituent on the other perpendicular porphyrin ring).
> Ultimately, I want to compute redox potentials at the QM/MM level, so I
> want to make sure the geometry is as good as possible. What are some ways I
> can improve my starting structure?
>
> Best,
> Matthew
>
>
>
>
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Received on Wed Dec 29 2021 - 12:00:02 PST
