Hi,
On Thu, Feb 27, 2014 at 6:14 AM, Jio M <jiomm.yahoo.com> wrote:
>
> This is indeed a nice suggestion and thanks for support. But I think
> theoreticaly also its not possible to achieve both at the same time (or its
> just me who can not think of this being possible theoreticaly!)
>
I could see doing it by including the z axis as an additional degree of
freedom in the rms fit. Of course, this still will result in structures
being "in-between" best-fit and z-axis-aligned...
In your suggestion, which is a good one, but in the last step the rms fit
> structures will not be best aligned to Z axis. Its only the reference
> structure which is best aligned to Z. In summary what I want to say: is it
> really possible to achieve both things together? I think Not possible, one
> has to sacrifice one thing!
>
Well, the reference structure will be aligned along Z, so all the other
structures should at least be somewhat aligned along Z (unless the
structure changes drastically from the reference). But you are right, the
structures will not be perfectly aligned to the Z axis.
> **********
> Just as a note for future searches in archive: I had to split cpptraj
> commands as it was not outputing trajout:
>
That's my fault - you need a second 'run' command at the bottom of the
original input. Then everything should complete in one session. Let me know
if that doesn't work.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Feb 27 2014 - 08:00:02 PST
