# AMBER Archive (2004)Subject: AMBER: principal axis

From: Alberto Perez (raist_at_mmb.pcb.ub.es)
Date: Wed Sep 15 2004 - 08:36:37 CDT

Hi,
We have been using ptraj to calculate the principal axis of
several macromolecules. After finding the inverse (transpose) of the principal
axis matrix, we plot the vectors on the reference frame of the molecule.
The resulting vectors do not seem to correspond to the real axis, we have
found that swapping of two of the rows and then inverting gives the
correct axis. Has this happened to any one else? Are we doing something

Here are the inputs (DNA molecule):

trajin DDD_pdb1d30.9991
prnlev 6
vector vector1 ~:1,12-13,24,25 principal x out vec1
vector vector1 ~:1,12-13,24,25 principal y out vec2
vector vector1 ~:1,12-13,24,25 principal z out vec3
go

and this is where ptraj says its swapping vectors:

JACOBI

Ixx = 710055.325 Iyy = 439416.500 Izz = 595414.288
Ixy = -90166.423 Ixz = -49156.317 Iyz = -188008.190

ATOM 1 XXX XX 1 22.034 22.563 31.039
ATOM 2 XXX XX 1 22.907 22.988 31.275
ATOM 1 YYY YY 2 22.034 22.563 31.039
ATOM 2 YYY YY 2 21.615 22.972 31.850
ATOM 1 ZZZ ZZ 3 22.034 22.563 31.039
ATOM 2 ZZZ ZZ 3 22.282 21.755 31.575

Eigenvalues 739265.601 716609.785 289010.727

transformVector PRINCIPAL AXIS:
ATOM 1 PP1 PP 1 22.034 22.563 31.039
ATOM 2 PP2 PP 1 22.282 21.755 31.575
PRINCIPAL, EIGENVECTORS/VALUES ARE SWAPPED: 0 2 1

```--
----------------------------------------------------------------
Alberto Perez
Molecular Modeling & Bioinformatics group
IRBB Parc Cientific de Barcelona | e-mail:raist_at_mmb.pcb.ub.es
Universitat de Barcelona         | phone: + 34 93 403 71 55
Josep Samitier,1-5               | FAX:   + 34 93 403 71 57
08028 Barcelona (Spain)          |
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