Hi Dave,
The simulated annealing constraints are all within 1 RNA nucleotide,
and I am just rotating a dihedral angle to try to satisfy 2-3 distance
constraints, which vary by each nucleotide.
I will check these programs out. Thanks for your advice!
-Dave
On 8/2/11, David A Case <case.biomaps.rutgers.edu> wrote:
> 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 - 11:00:02 PDT
