Dear Albert,
You might want to check out the software developed by Wales and co-workers
(GMIN, OPTIM, and PATHSAMPLE) to build the energy landscape. If the ligand
you are studying is not too big you will be able to create a
'Disconnectivity' graph showing the energy landscape of that particular
system. Check out the following paper where we applied Discrete Path
Sampling method to study RNA CUG repeat expansions.
Yildirim, I.,* Chakraborty, D., Disney, M. D., Wales, D. J., and Schatz,
G. C., “Computational Investigation of RNA CUG repeats responsible for
Myotonic Dystrophy 1”, J. Chem. Theory Comput. 11, 4943–4958, 2015.
Best regards,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Website: http://ilyasyildirim.wordpress.com =
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http://www.linkedin.com/in/yildirimilyas =
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http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
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On Sun, 26 Jun 2016, Albert wrote:
> Hello:
>
> I've got a ligand and I am just wondering is there any MM (not MD) tool
> in Amber to sample ligand conformation?
>
> Thank you very much.
>
> Albert
>
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Received on Sun Jun 26 2016 - 12:00:02 PDT
