Hi,
In general, simply plotting some histograms of certain dihedrals of
interest can give you some information on whether the dihedral angle
is rapidly changing conformations or not. E.g. using the following
cpptraj input:
dihedral chi2 :2.N :2.CA :2.CB :2.CG out chi2.agr
hist chi2,-180,180,30,* out chi2.hist.agr
On Thu, Apr 4, 2013 at 4:10 AM, anu chandra <anu80125.gmail.com> wrote:
> 1. Does side chain dihedral angle ( Calpha-Cbeta and Cbeta-Cgamma) order
> parameters can provided some information about conformational changes? If
> so, does Amber (cpptarj/ptraj) have a way to calculate the same?
If you have J-coupling values for your system, you can calculate
J-coupling values from dihedrals in your system using the cpptraj
command 'jcoupling'.
> 2. Even though there are publications, which report about the backbone
> dihedral angle PCA calculations, on a similar line, is it possible to do
> side-chain dihedral angle PCA? And how Amber can help me in this?
In principal I don't see why you couldn't do dihedral PCA on sidechain
dihedrals (or any other dihedrals). Cpptraj cannot do this yet,
although this functionality is planned for the future. I believe there
are currently other programs out there that will let you do this
analysis.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Apr 05 2013 - 09:30:03 PDT
