# Re: [AMBER] principal axes calculation in ptraj

From: Asmita Gupta <asmita4des.gmail.com>
Date: Wed, 20 Aug 2014 13:15:37 +0530

okay...so can we assume that X vector represents eigenvector with largest
eigenvalue and Z with least??

If i want to calculate angle between two X vectors (of different subsets of
residues), can that be done using simple vector algebra (dot product
method?)

Thanks

On Tue, Aug 19, 2014 at 8:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> Yes, the principal axes of coordinates are calculated as the
> eigenvectors resulting from diagonalization of the mass-weighted
> covariance matrix for the specified set of XYZ coordinates.
>
> Crankshaft analysis is essentially looking for anti-correlated motion
> between two data sets. In cpptraj the 'crankshaft' analysis is really
> primarily intended to look at crankshaft motion of distances and
> dihedrals (and more specifically dihedrals in DNA), not vectors (I
> realize this is not documented, sorry; I will need to correct this).
> For example, in DNA the alpha/gamma pair of torsions usually moves in
> an anti-correlated fashion.
>
> Hope this helps,
>
> -Dan
>
> On Tue, Aug 19, 2014 at 3:12 AM, Asmita Gupta <asmita4des.gmail.com>
> wrote:
> > Dear users,
> >
> > I have a protein of 974 residues. I want to calculate principal axes for
> a
> > set of residues using principle command in ptraj. This is my script:
> >
> > trajin ../../frun.crd 1 last 3
> >
> > center :1-974 mass origin
> > image origin center familiar
> >
> > vector v1_h1 principal x out pa1_h1.dat :1-35.CA
> > vector v2_h1 principal y out pa2_h1.dat :1-35.CA
> > vector v3_h1 principal z out pa3_h1.dat :1-35.CA
> >
> > vector v1_h2 principal x out pa1_h2.dat :40-60.CA
> > vector v2_h2 principal y out pa2_h2.dat :40-60.CA
> > vector v3_h2 principal z out pa3_h2.dat :40-60.CA
> >
> > crank angle v3_h1 v3_h2 out ang_h1h2_v3.dat results outz_v1_2.dat
> >
> ------------------------------------------------------------------------------------
> >
> > I want to ask how this axes calculation is done in AMBER? As in Gromacs,
> > this kind of calculation involves doing a PCA of the subset of residues
> and
> > generating axes vectors. Is the same method followed in AMBER??
> >
> > How does X,Y and Z vectors are determined??
> >
> > What is the meaning of "crank" angle between two vectors (i referred the
> > manual, but couldn't understand the meaning...).
> >
> >
> > Thank you
> >
> >
> > Asmita
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Aug 20 2014 - 01:00:02 PDT
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