Dear Daniel,
Thanks for your valuable reply. I have used 2500 frames for the
calculation. I have attached the ptraj input/output files for your
reference. BYW, I couldn't get what you mean by - ' what does the
underlying trajectory look like? '. I am using Amber 9.0 for the simulation
and AmberTools-12 for analysis.
Once again thanking you for the reply.
Regards
Anu
On Fri, Apr 5, 2013 at 9:08 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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>
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- application/octet-stream attachment: S2_NH.log
Received on Mon Apr 08 2013 - 02:00:03 PDT
