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
Received on Thu Sep 06 2012 - 21:30:03 PDT
