Hi,
.Daniel, thanks for you immediate reply and I will definitely try with the
analysis you suggested.
Please let me know if any one comes to know about any program, which helps
to calculate dihedral angle PCA.
Thanks in advance
Regards
Anu
On Fri, Apr 5, 2013 at 9:57 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 Mon Apr 08 2013 - 02:00:03 PDT
