From: John Stone (
Date: Fri Dec 20 2013 - 16:03:08 CST

I would think you'd get the same principal axis if there is no
difference other than translation of identical structure to a new
origin, but without more information it's hard to say what may
have gone wrong in your specific case.

  John Stone

On Sat, Dec 21, 2013 at 01:39:28AM +0530, wrote:
> Hi all,
> I have prepared a system with two identical molecules placed with
> exactly the same orientation at some distance . When I calculate the
> principal axis vectors using Orient, I see that the the corresponding
> principal axis vectors of the two molecules are not parallel to each
> other (principal axis 1 of molecule 1 is not parallel to principal axis
> 1 of molecule 2 and so on). Shouldn't they be parallel, if the
> molecules are exactly the same and have the same orientation? If not,
> then why?? Kindly guide me on this.
> Thanks.
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349