Hi thanks for your answers
I am studying a reaction mechanism in a protein.
I am not sure if I have to use hybrid quantum-classical simulations.
Or use Amber and compute the free energy profile for a reaction
mechanism, does Amber treat reaction mechanisms??
Thanks
Regards
B
On 16 Jul 2008, at 15:10, Adrian Roitberg wrote:
> Hi all,
>
> Let's be careful here !
> A free energy profile is not a well defined quantity per-se, and
> MMPBSA is really useful for binding free energies.
>
> So, Boutheina, we need much more data about what you mean.
>
> a.
>
>
> Christopher Gaughan wrote:
>> If you have a trajectory you could use the mm-pbsa module in
>> Amber. Look at
>> mm-pbsa tutorial on amber tutorial website
>> CG
>> On Wed, Jul 16, 2008 at 11:54 AM, Boutheina Kerkeni
>> <b.kerkeni.ucl.ac.uk>
>> wrote:
>>> Hi
>>>
>>> Does any one knows how to compute the free energy profile with
>>> Amber?
>>> Thanks
>>> Regards
>>> Boutheina
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>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Sun Jul 20 2008 - 06:07:14 PDT
