- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

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)
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Aug 20 2014 - 01:00:02 PDT

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:

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Aug 20 2014 - 01:00:02 PDT

Custom Search