What do you mean "energy landscape"? The full "energy landscape" is a
massive beast ([3N-6]-dimensional, where N is the number of atoms), which
is impossible to visualize in 2 or 3 dimensions. The best you can do to
look at an "energy landscape" is to define some kind of coordinate or order
parameter or a combination of 2 of these (e.g. radius of gyration, RMSd, a
distance between two atoms/groups of atoms, an angle between 3 atoms, etc.)
and look at the free energy surface of those coordinates/parameters
averaged over every other degree of freedom (a so-called potential of mean
force, or PMF).
There are a number of ways of generating these PMFs, like steered MD with
Jarzynsky's equation, umbrella sampling coupled with WHAM to name a few.
There is a section of the Amber manual devoted to free energy calculations
along with associated references. That is probably a good place to start.
HTH,
Jason
On Fri, Feb 3, 2012 at 4:34 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
> Any reference on the use of AMBER to study the energy landscape of a
> protein structure?
> In addition to AMBER, do we need additional software to do the energy
> landscape calculation?
> Best regards,
> Catherine
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Feb 03 2012 - 11:30:02 PST
