Hi,
On Fri, Apr 5, 2013 at 1:16 AM, anu chandra <anu80125.gmail.com> wrote:
> ****************************************************************
> Eigenvector file: IRED
> 5 5
> 1.00000 1.00000 1.00000 1.00000 1.00000
It's OK for the first line in the 'modes' file to be all one in this
case - these are the average lengths (magnitudes) of your vectors,
which are normalized to 1.
> vector S2
> ----------------------
> 0 1.00000
> 1 1.00000
> 2 1.00000
> 3 1.00000
> 4 1.00000
How many frames are using in your calculation, and what does the
underlying trajectory look like? It may help if you attach your
complete ptraj input/output. An S2 parameter of 1.0 means essentially
no local motion, so if your protein is rigid this could be an OK
result. The fact that you obtain similar results with a different set
of vectors makes me suspect there is something going on in the
underlying trajectory.
-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) 585-9119 (Fax)
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Received on Fri Apr 05 2013 - 09:00:03 PDT
