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)
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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--
-------------------------
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 Mon Apr 08 2013 - 10:30:02 PDT
