Re: AMBER: principal axis

From: Thomas E. Cheatham, III <>
Date: Wed, 15 Sep 2004 09:41:37 -0600 (Mountain Daylight Time)

> 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
> wrong? Thanks in advance.

The swapping of vectors in ptraj w/ principal is done since when viewing
movies of the motion for molecules which have two axes that are similar
(like DNA with one long axis and two similar short axes), occasionally the
molecule would "jump" since the X and Y vectors (where Z is the long)
would flip. Based on an old CCL (comp chem mailing list) post and code
for principal axis, I implemented a means to check for this inversion of
the vectors. It is in the routine jacobiCheckChirality() in actions.c of
the ptraj source. It is definately possible that this is not "correct",
however empirically it removed the jumping/inverting eigenvalue problem.

To avoid the swapping, you can comment out the call to
jacobiCheckChirality(). I should make this an input option.

If you've got a better/correct solution, please let me know :-)


\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
| (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418

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Received on Wed Sep 15 2004 - 16:53:01 PDT
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