On Tue, Aug 02, 2011, David Condon wrote:
>
> For the last year or so I have been using simulated annealing to attempt to
> satisfy NMR restraints. However, this has been highly impractical for what
> I want.
>
> I am not interested in any of the energy, the heating, the cooling cycle,
> etc in a simulated annealing protocol. I simply want to move the molecule
> to satisfy distance constraints. I used to do this with a model kit, ruler,
> and a protractor but my adviser doesn't care for such a low-tech approach.
>
> Is anyone aware of a computational protocol to do this, Amber or otherwise?
It's not clear what size molecule you are talking about. The
comment about a protractor makes it sound like a fairly small
one(?). Furthermore, you don't say why simulated annealing is "highly
impractical". Annealing is a bit of a blunt tool, but has been used for
this purpose for decades (since the mid-80's), and is rather robust. For
some systems you might want to consider distance geometry, as found (among
other places) in NAB, Tinker, or X-PLOR.
....dac
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Received on Tue Aug 02 2011 - 09:30:03 PDT
