Hi,
The first two numbers are number of average coordinates and number of
coordinates in each eigenvector respectively. The next section of
numbers are the average coordinates. The sections following '***' give
the number and eigenvalue of each eigenvector, followed by the coords
of the eigenvector. For some more info see the 'Correlation and
fluctuation facility' part of the 'ptraj' section of the manual.
To calculate atomic fluctuations see the 'atomicfluct' command.
-Dan
On Thu, Sep 6, 2012 at 10:09 PM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>
> Thanks Dan for reply
>
> using command: matrix covar name cacovar @CA out cacovar.dat
> I have got matrix then I analyze it using command: analyze matrix cacovar out
> eigen_vectors.dat vecs 2
> this gave me eignvector, header of eigen_vectors.dat file is look like this:
>
> Eigenvector file: COVAR
> 174 174
>
> This is follow by numbers:
> 38.48036 12.72356 30.40956 36.40916 13.86220 33.34885 32.80080
> 12.65712 33.59961 30.52444 15.41233 32.47719 28.46585 17.41237
> 34.90833 25.29844 19.21666 34.30532 24.18775 22.48056 35.74431
> ------
> --------
> ****
> 1 531.95240
> 0.03007 0.00077 0.01337 0.02274 0.01284 0.00620 0.02810
> -0.00378 0.00747 0.01524 -0.01853 -0.01482 0.00389 -0.01189
> -0.02649 -0.00443 -0.03142 -0.04068 -0.02354 -0.02577 -0.06252
> ------
> ------
> ****
> 2 323.90815
> -0.07566 -0.00091 -0.01731 -0.06728 -0.01324 -0.00726 -0.06374
> -0.01849 0.00399 -0.07227 -0.02386 0.01563 -0.06464 -0.03032
> 0.02669 -0.07514 -0.05743 0.04366 -0.08307 -0.06158 0.04018
> -------
> -------
>
> How I define all thses contents of eignvector file.
>
> Next how I can plot residue-residue fluctuation of alpha carbon.
>
>
>
>> Hi,
>>
>> Per the manual, you should be able to specify a mask of the atoms you
>> want to the matrix command, e.g.:
>>
>> matrix covar name cacovar .CA
>>
>> Let me know if that doesn't work for you.
>>
>> -Dan
>>
>> On Thu, Sep 6, 2012 at 9:53 AM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>>>
>>> Hello all
>>> I want to do PCA analysis for residue - residue fulctuation of alpha carbon.
>>> I go through the Correlation and fluctuation facility in AmberTool and also the
>>> amber mailing list. There is matrix command to generate covariance matrix but
>>> it
>>> generate covariance matrix byatom.
>>>
>>> How I can gerenate residue - residue fulctuation map of alpha carbon using
>>> covvariance matrix?
>>>
>>>
>>> With regards
>>>
>>>
>>> Sangita Kachhap
>>> SRF
>>> BIC,IMTECH
>>> CHANDIGARH
>>>
>>> ______________________________________________________________________
>>> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
>>> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
>>> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
>>> पिन कोड/PIN CODE :160036
>>> दूरभाष/EPABX :0172 6665 201-202
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> 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
>>
>
>
> Sangita Kachhap
> SRF
> BIC,IMTECH
> CHANDIGARH
>
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202
>
> _______________________________________________
> AMBER mailing list
> 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
Received on Fri Sep 07 2012 - 14:30:03 PDT
