I try to specify my question.
I suppose that force field based simulated annealing with positions
restraints applied to the all protein atoms but not for loops which I'd
like to refine might be exactly what I'm looking for. Could someone suggest
appropriate SA setups for such loop refirement: e.g I'm interesting in
number of SA windows, coupling constants in each windows, appropriate
implicit solvent models?
James
2014-05-26 14:06 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> Dear Amber's users!
>
>
> I need to refine some flexible regions (mainly long loop and linker
> regions) of my proteins prior to the production MD run using some enhanced
> sampling engines implemented in Amber like accelerated molecular dynamics
> or simulated annealing. Please provide me with some basic ideas of the
> easiliest realization of these methods in amber including suitable implicit
> solvent models for such task with the tutorials and further reading.
>
>
> TFH,
>
> James
>
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Received on Wed May 28 2014 - 01:00:02 PDT
