Re: [AMBER] principal axes calculation in ptraj

From: Daniel Roe <>
Date: Tue, 19 Aug 2014 08:50:28 -0600


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,


On Tue, Aug 19, 2014 at 3:12 AM, Asmita Gupta <> 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

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Aug 19 2014 - 08:00:03 PDT
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