Dear Daniel,
Thanks for the reply. Now, as a trial run if I do with 6 vectors, I can
able to get the S2 order parameter, which seems to be reliable. Here is the
the part of output looks...
*************************************************
PTRAJ: Analyzing accumulated data
************************************
- Calculated iRed order parameters -
************************************
vector S2
----------------------
0 0.98037
1 0.99997
2 0.95542
3 0.99089
4 0.96454
5 0.99974
**************************************************
Thanks and regards
Anu
On Mon, Apr 8, 2013 at 10:55 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I should have noticed this before, but you are only using 5 vectors
> and therefore calculating 5 eigenmodes. The S2 order parameter is
> calculated according to eq 6. from Prompers & Brueschweiler JACS
> (2002) v124 p4522-4534, where the sum in that equation extends only
> over the internal modes (i.e. modes 1-5 are not used). Since you only
> have 5 modes, the S2 parameters all come out to be 1. You should
> define and calculate an N-H vector for every N-H present in your
> protein for use with IRED analysis (the easiest way to do that is
> probably with a script).
>
> -Dan
>
> On Fri, Apr 5, 2013 at 11:48 PM, anu chandra <anu80125.gmail.com> wrote:
> > 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)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 09 2013 - 00:00:02 PDT
